Build sequences for mechanosynthesis

ABSTRACT

Methods for creating build sequences which are determined using computational chemistry algorithms to simulate mechanosynthetic reactions, and which may use the mechanosynthesis process conditions or equipment limitations in these simulations, and which facilitate determining a set of mechanosynthetic reactions that will build an atomically-precise workpiece with a desired degree of reliability. Included are methods for error correction of pathological reactions or avoidance of pathological reactions. Libraries of reactions may be used to reduce simulation requirements.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of, and claims priority to,pending application Ser. No. 14/712,506, filed 14 May 2015, which is acontinuation-in-part, and claims priority to, pending applicationPCT/US13/28419, filed 28 Feb. 2013. Pending application Ser. No.14/712,506 is hereby incorporated by reference.

FEDERALLY SPONSORED RESEARCH

Not applicable.

SEQUENCE LISTING OR PROGRAM

Not applicable.

TECHNICAL FIELD

The present application relates to mechanosynthesis, the fabrication ofatomically precise tools and materials using individual atoms or smallgroups of atoms as the fundamental building blocks, and moreparticularly, to devices, methods and systems for performing orderedsequences of site-specific positionally controlled chemical reactionsthat are induced by use of mechanical force.

BACKGROUND OF THE INVENTION

Mechanosynthesis and Related Techniques

Scanning Probe Microscopy (SPM, in which we include all relatedtechniques such as AFM, STM and others) laboratories have beenmanipulating individual atoms and molecules for decades. (Eigler andSchweizer, “Positioning Single Atoms with a Scanning TunnellingMicroscope,” Nature. 1990. 344:524-526; Eigler, Lutz et al., “An atomicswitch realized with the scanning tunneling microscope,” Nature. 1991.352:600-603; Stroscio and Eigler, “Atomic and Molecular Manipulationwith the Scanning Tunneling Microscope,” Science. 1991. 254:1319-1326;Meyer, Neu et al., “Controlled lateral manipulation of single moleculeswith the scanning tunneling microscope,” Applied Physics A. 1995.60:343-345; MEYER, NEU et al., “Building Nanostructures by ControlledManipulation of Single Atoms and Molecules with the Scanning TunnelingMicroscope,” phys Stat Sol (b). 1995. 192:313-324; Bartels, Meyer etal., “Basic Steps of Lateral Manipulation of Single Atoms and DiatomicClusters with a Scanning Tunneling Microscope Tip,” PHYSICAL REVIEWLETTERS. 1997. 79:697-700; Bartels, Meyer et al., “Controlled verticalmanipulation of single CO molecules with the scanning tunnelingmicroscope: A route to chemical contrast,” Applied Physics Letters.1997. 71:213; Huang and Yamamoto, “Physical mechanism of hydrogendeposition from a scanning tunneling microscopy tip,” Appl. Phys. A.1997. 64:R419-R422; Bartels, Meyer et al., “Dynamics of Electron-InducedManipulation of Individual CO Molecules on Cu(111),” PHYSICAL REVIEWLETTERS. 1998. 80; Ho and Lee, “Single bond formation andcharacterization with a scanning tunneling microscope,” Science1999.1719-1722; Hersam, Guisinger et al., “Silicon-based molecularnanotechnology,” Nanotechnology. 2000; Hersam, Guisinger et al.,“Silicon-based molecular nanotechnology,” Nanotechnology. 2000. 11:70;Hla, Bartels et al., “Inducing All Steps of a Chemical Reaction with theScanning Tunneling Microscope Tip—Towards Single Molecule Engineering,”PHYSICAL REVIEW LETTERS. 2000. 85:2777-2780; Lauhon and Ho, “Control andCharacterization of a Multistep Unimolecular Reaction,” PHYSICAL REVIEWLETTERS. 2000. 84:1527-1530; Oyabu, Custance et al., “Mechanicalvertical manipulation of selected single atoms by soft nanoindentationusing near contact atomic force microscopy,” Phys. Rev. Lett. 2003. 90;Basu, Guisinger et al., “Room temperature nanofabrication of atomicallyregistered heteromolecular organosilicon nanostructures using multistepfeedback controlled lithography,” Applied Physics Letters. 2004.85:2619; Morita, Sugimoto et al., “Atom-selective imaging and mechanicalatom manipulation using the non-contact atomic force microscope,” J.Electron Microsc. 2004. 53:163-168; Ruess, Oberbeck et al., “TowardAtomic-Scale Device Fabrication in Silicon Using Scanning ProbeMicroscopy,” Nano Letters. 2004. 4; Stroscio and Celotta, “Controllingthe Dynamics of a Single Atom in Lateral Atom Manipulation,” Science.2004. 306:242-247; Duwez, Cuenot et al., “Mechanochemistry: targeteddelivery of single molecules,” Nature Nanotechnology. 2006. 1:122-125;Iancu and Hla, “Realization of a four-step molecular switch in scanningtunneling microscope manipulation of single chlorophyll-a molecules,”Proc Natl Acad Sci USA. 2006. 103:13718-21; Ruess, Pok et al.,“Realization of atomically controlled dopant devices in silicon,” Small.2007. 3:563-7; Sugimoto, Pou et al., “Complex Patterning by VerticalInterchange Atom Manipulation Using Atomic Force Microscopy,” Science.2008. 322:413-417; Randall, Lyding et al., “Atomic precision lithographyon Si,” J. Vac. Sci. Technol. B. 2009; Owen, Ballard et al., “Patternedatomic layer epitaxy of Si/Si(001):H,” Journal of Vacuum Science &Technology B: Microelectronics and Nanometer Structures. 2011.29:06F201; Wang and Hersam, “Nanofabrication of heteromolecular organicnanostructures on epitaxial graphene via room temperaturefeedback-controlled lithography,” Nano Lett. 2011. 11:589-93; Kawai,Foster et al., “Atom manipulation on an insulating surface at roomtemperature,” Nat Commun. 2014. 5:4403) These efforts have generallybeen limited to simple one- or two-dimensional structures, but thetechniques are powerful enough to have already demonstrated basicmolecular-scale logic (Heinrich, Lutz et al., “Molecule Cascades,”Science. 2002. 298:1381-1387) and to have inspired commercial efforts tobuild atomically-precise structures, including work towards quantumcomputers. (Ruess, Oberbeck et al., “Toward Atomic-Scale DeviceFabrication in Silicon Using Scanning Probe Microscopy,” Nano Letters.2004. 4; Ruess, Pok et al., “Realization of atomically controlled dopantdevices in silicon,” Small. 2007. 3:563-7; Randall, Lyding et al.,“Atomic precision lithography on Si,” J. Vac. Sci. Technol. B. 2009.)

Previously, atom manipulation was performed using one of threetechniques: Feedback Controlled Lithography (FCL), horizontal atommanipulation, or vertical atom manipulation. FCL uses a scanning probetip to remove atoms (e.g., passivating hydrogens) from a surface,creating chemically-reactive radical patterns on that surface, followedby bulk chemical reactions that take advantage of the new radical sitesto create a surface modified at specific atomic locations. Horizontalatom manipulation relies upon dragging atoms across flat surfaces toplace them at specific locations, in effect decorating a surface withatomically-precise designs. Vertical atom manipulation, often referredto as mechanosynthesis, includes the deposition of single atoms ormolecules, such as CO, as well as vertical atom interchange, whichallows a surface and tip atom to be swapped. (Oyabu, Custance et al.,“Mechanical vertical manipulation of selected single atoms by softnanoindentation using near contact atomic force microscopy,” Phys. Rev.Lett. 2003. 90; Morita, Sugimoto et al., “Atom-selective imaging andmechanical atom manipulation using the non-contact atomic forcemicroscope,” J. Electron Microsc. 2004. 53:163-168; Oyabu, Custance etal., “Mechanical Vertical Manipulation of Single Atoms on theGe(111)-c(2×8) Surface by Noncontact Atomic Force Microscopy,” SeventhInternational Conference on non-contact Atomic Force Microscopy.Seattle, Wash. 2004.34; Sugimoto, Pou et al., “Complex Patterning byVertical Interchange Atom Manipulation Using Atomic Force Microscopy,”Science. 2008. 322:413-417; Tarasov, Akberova et al., “Optimal TooltipTrajectories in a Hydrogen Abstraction Tool Recharge Reaction Sequencefor Positionally Controlled Diamond Mechanosynthesis,” J. Comput. Theor.Nanosci. 2010. 7:325-353; Herman, “Toward Mechanosynthesis of DiamondoidStructures: IX Commercial Capped CNT Scanning Probe Microscopy Tip asNowadays Available Tool for Silylene Molecule and Silicon AtomTransfer,” Journal of Computational and Theoretical Nanoscience. 2012.9:2240-2244; Herman, “Toward Mechanosynthesis of Diamondoid Structures:X. Commercial Capped CNT SPM Tip as Nowadays Available C2 DimerPlacement Tool for Tip-Based Nanofabrication,” Journal of Computationaland Theoretical Nanoscience. 2013. 10:2113-2122; Kawai, Foster et al.,“Atom manipulation on an insulating surface at room temperature,” NatCommun. 2014. 5:4403)

As previously implemented, each of these atom manipulation techniquesmodifies a single atomic layer on a surface, does so using a verylimited palette of reactions and reactants, and cannot manufacturecomplex, three-dimensional products.

Previous work by the current inventors, including U.S. Pat. No.8,171,568, U.S. Pat. No. 8,276,211, U.S. Pat. No. 9,244,097, US PatentApplication 20150355228, US Patent Application 20160167970 and PCTApplication WO/2014/133529 sought to address some of the shortcomings ofprior atom manipulation techniques via improved implementations ofmechanosynthesis. These references describe various aspects ofmechanosynthesis, including a bootstrap process for preparingatomically-precise tips from non-atomically-precise tips, reactions thatcan be used to build three-dimensional workpieces, methods for orderingsuch reactions into build sequences, provisioning of feedstock, anddisposal of waste atoms.

Nonetheless, room for improvement still exists. Accordingly, it is anobject of the invention to improve the manufacturing ofthree-dimensional workpieces via mechanosynthesis.

BRIEF SUMMARY OF THE INVENTION

The present invention is directed to processes for creating buildsequences which are determined using computational chemistry algorithmsto simulate mechanosynthetic reactions, and which may use themechanosynthesis process conditions or equipment limitations in thesesimulations, and which facilitate determining a set of mechanosyntheticreactions that will build an atomically-precise workpiece with a desireddegree of reliability. Included are methods for error correction ofpathological reactions or avoidance of pathological reactions. Librariesof reactions may be used to reduce simulation requirements.

BRIEF DESCRIPTION OF DRAWINGS

For a more complete understanding of the present invention, reference isnow made to the following descriptions taken in conjunction with theaccompanying drawings, in which:

FIG. 1 depicts the modular parts of an exemplary tip.

FIG. 2 depicts the modular parts of another exemplary tip.

FIG. 3 depicts the AbstractionO tip surface-mounted on Silicon.

FIG. 4 depicts the HDonationO tip surface-mounted on Silicon.

FIG. 5 depicts the C2DonationO tip surface-mounted on Silicon.

FIG. 6 depicts the MeDonationO tip surface-mounted on Silicon.

FIG. 7 depicts a tip surface-mounted on Silicon which can beSiH3DonationO, GeH3DonationO, SiMe3DonationO or GeMe3DonationO.

FIG. 8 depicts the AbstractionNH tip surface-mounted on Silicon.

FIG. 9 depicts the HDonationNH tip surface-mounted on Silicon.

FIG. 10 depicts the C2DonationNH tip surface-mounted on Silicon.

FIG. 11 depicts the MeDonationNH tip surface-mounted on Silicon.

FIG. 12 depicts a tip surface-mounted on Silicon which can beSiH3DonationNH, GeH3DonationNH, SiMe3DonationNH or GeMe3DonationNH.

FIG. 13 depicts the AbstractionS tip surface-mounted on Gold.

FIG. 14 depicts the HDonationS tip surface-mounted on Gold.

FIG. 15 depicts the C2DonationS tip surface-mounted on Gold.

FIG. 16 depicts the MeDonationS tip surface-mounted on Gold.

FIG. 17 depicts a tip surface-mounted on Silicon which can beSiH3DonationS, GeH3DonationS, SiMe3DonationS or GeMe3DonationS.

FIG. 18 depicts a synthetic route for the AbstractionO tip.

FIG. 19 depicts a synthetic route for the HDonationO tip.

FIG. 20 depicts a synthetic route for the C2DonationO tip.

FIG. 21 depicts a synthetic route for the MeDonationO tip.

FIG. 22 depicts a synthetic route for the SiH3DonationO tip.

FIG. 23 depicts a synthetic route for the GeH3DonationO tip.

FIG. 24 depicts a synthetic route for the SiMe3DonationO tip.

FIG. 25 depicts a synthetic route for the GeMe3DonationO tip.

FIG. 26 depicts a synthetic route for the AbstractionNH tip.

FIG. 27 depicts a synthetic route for the HDonationO tip.

FIG. 28 depicts a synthetic route for the C2DonationO tip.

FIG. 29 depicts a synthetic route for the MeDonationO tip.

FIG. 30 depicts a synthetic route for the SiH3DonationO tip.

FIG. 31 depicts a synthetic route for the GeH3DonationO tip.

FIG. 32 depicts a synthetic route for the SiMe3DonationO tip.

FIG. 33 depicts a synthetic route for the GeMe3DonationO tip.

FIG. 34 depicts a synthetic route for the AbstractionS tip.

FIG. 35 depicts a synthetic route for the HDonationS tip.

FIG. 36 depicts a synthetic route for the C2DonationS tip.

FIG. 37 depicts a synthetic route for the MeDonationS tip.

FIG. 38 depicts a synthetic route for the SiH3DonationS tip.

FIG. 39 depicts a synthetic route for the GeH3DonationS tip.

FIG. 40 depicts a synthetic route for the SiMe3DonationS tip.

FIG. 41 depicts a synthetic route for the GeMe3DonationS tip.

FIG. 42 depicts a synthetic route for the FHD-104X intermediate.

FIG. 43 depicts a synthetic route for the NHD-103X intermediate.

FIG. 44 depicts photo-activation of a halogen-capped tip.

FIG. 45 depicts photo-activation of a Barton ester-capped tip.

FIG. 46 depicts an exemplary synthesis of a tip with Barton ester cap.

FIG. 47 depicts the use of surface-mounted tips where the workpiecemoves.

FIG. 48 depicts the use of surface-mounted tips where the surface moves.

FIG. 49 depicts a metrology setup for measuring six degrees of freedom.

FIG. 50a-f depicts a way of implementing the sequential tip method.

FIG. 51 depicts a conventional mode tip that can be used for thesequential tip method.

FIG. 52a-o depicts a build sequence for building a half-Si-Rad tip.

FIG. 53 depicts a synthetic pathway for synthesizing an AdamRad-Br tip.

FIG. 54a-d depicts exemplary methods of using strain to alter affinity.

FIG. 55 is a flowchart of an exemplary process for specifying aworkpiece.

FIG. 56 is a flowchart of an exemplary process for designing reactions.

FIG. 57 is a flowchart of an exemplary process for performing reactions.

FIG. 58 is a flowchart of an exemplary process for testing reactionoutcomes.

DETAILED DESCRIPTION OF THE INVENTION Definitions

The following definitions are used herein:

An “adamantane” molecule comprises a 3D cage structure of ten carbonatoms, each terminated with one or two hydrogen atoms, having thechemical formula C10H16 in its fully hydrogen-terminated form.Adamantane is the smallest possible unit cage of crystalline diamond.

An “adamantane-like” structure includes one or more adamantanes, one ormore adamantanes where one or more atoms have been substituted withatoms or molecular fragments of like or similar valence, including e.g.,Nitrogen, Oxygen, and Sulfur-substituted variations, and similarmolecules comprising polycyclic or cage-like structures. By way ofexample, and not of limitation, adamantane-like structures would includeadamantane, heteroadamantanes, polymantanes, lonsdaleite, crystallinesilicon or germanium, and versions of each of the foregoing where, forexample, Fluorine or another halogen is used for termination instead ofHydrogen, or where termination is incomplete.

An “aperiodic” workpiece is one where the overall shape or atomicconstituents do not result directly from the crystal structure orlattice of the workpiece. For example, diamond crystals tend to form anoctahedral shape due to the bond angles of the underlying atoms. Anoctahedral diamond crystal, or variations thereof, could be said to beperiodic because both the internal structure and the external shape isdetermined by the periodic structure of the crystal. On the other hand,a diamond shaped like a car cannot be said to be periodic because,internal structure aside, there is no way the lattice cell of diamondcould have specified the shape of a car. Another example of aperiodicdiamond would be a crystal composed largely of diamond, but withirregular (with respect to the crystal matrix) substitutions made withinits matrix, such as the replacement of some carbon atoms with silicon orgermanium. Almost any complex shape or part is going to be aperiodicbecause of its shape, its atomic constituents, or both. Note thataperiodic does not necessarily mean irregular. Take, for example, aconventional gear made of diamond. The round, symmetrical shape of agear and its teeth are radially symmetric and have a kind ofperiodicity. However, this periodicity is not derived from theunderlying crystal structure. For a structure to be periodic, it is notenough that it be regular; it must be regular in a manner that isderived from its crystal structure. While this definition may seempedantic, it is useful when discussing the differences between anengineered, atomically-precise material versus a naturally-occurring orbulk-synthesized crystal. Naturally-occurring or bulk-synthesizedcrystals are generally, impurities or bonding errors notwithstanding,periodic structures. There is no way know to the authors to make themboth atomically-precise and aperiodic since their method of manufactureinherently relies upon the periodic crystal structure given elementsform under a particular set of conditions, rather than controlling thestructure atom by atom as can be done with a positionally-controlledtechnology like mechanosynthesis.

An “atom” includes the standard use of the term, including a radical,which, for example, may be just a proton in the case of H⁺.

“Atomically-precise” in the context of a reaction means where theposition and identity of each atom is known to a precision adequate toenable the reaction to be directed to a particular atomic site(“site-specific”). In the context of a workpiece, atomically-preciserefers to the actual molecular structure being identical to thespecified structure (e.g., as specified by a molecular model or buildsequence).

The “bridgehead” position in an adamantane-like molecular structurerefers to a structural atom that is bonded to three other structuralatoms and may be terminated by one or more nonstructural atoms. This iscontrasted with a “sidewall” position which refers to a structural atomthat is bonded to two other structural atoms and is terminated by one ormore nonstructural atoms.

A “build sequence” is one or more mechanosynthetic reactions arranged inan ordered sequence that permits the assembly, disassembly, ormodification of a workpiece.

A “chemical bond” is an interatomic covalent bond, an interatomic ionicbond, or interatomic coordination bond, as these terms are commonlyunderstood by practitioners skilled in the art.

A “chemical reaction” is said to occur when chemical bonds are formed,broken, or altered.

“Conventional mode” is where one or more tips are affixed to apositional means/device (e.g., an SPM probe) to facilitatemechanosynthetic reactions between the tips and a workpiece. Thiscontrasts with “inverted mode” where a workpiece is affixed to apositional means and the workpiece moves to the tips. Although uncommonin practice, since in theory both tips and workpiece could be affixed toa positional means, another way to distinguish between the modes wouldbe to say that if the workpiece is connected to apparatus whichindicates that the workpiece is being used as a probe (e.g., if STM isbeing done through the workpiece), the system is operating in invertedmode. Otherwise, the system is operating in conventional mode.Conventional mode tips are generally affixed to a positional meanssingly or in small numbers, while in inverted mode, a larger, generallystationary, presentation surface allows the provisioning of largenumbers of surface-mounted tips. Note that although inverted mode andsurface mounted tips may be used together, inverted mode should not beconflated with surface-mounted tips. As is described herein (thesequential tip method), surface-mounted tips can be used in a systemwhich is operating in conventional mode.

A “conventional mode tip” is a tip affixed to a positional means orotherwise being employed in conventional mode as described in thatdefinition, just as an “inverted mode tip” is a tip affixed to apresentation surface or otherwise being employed in “inverted mode” asdescribed in that definition.

“Diamond” is a crystal of repeating adamantane cage units arranged invarious well-known crystallographic lattice geometries.

“Diamondoid” materials include any stiff covalent solid that is similarto diamond in strength, chemical inertness, or other important materialproperties, and possesses a three-dimensional network of bonds. Examplesof such materials include but are not limited to (1) diamond, includingcubic and hexagonal lattices and all primary and vicinalcrystallographic surfaces thereof, (2) carbon nanotubes, fullerenes, andother graphene structures, (3) several strong covalent ceramics of whichsilicon carbide, silicon nitride, and boron nitride are representative,(4) a few very stiff ionic ceramics of which sapphire (monocrystallinealuminum oxide) is representative, and (5) partially substitutedvariants of the above that are well-known to those skilled in the art.

“Feedstock” is the supply of atoms used to perform mechanosyntheticreactions. Feedstock may take the form of one or more atoms, includingradicals (e.g., .GeH2, .CH2). Feedstock includes atoms removed from aworkpiece. For example, a hydrogen atom from a workpiece may be thefeedstock for a hydrogen abstraction tip. In such cases, sincefrequently nothing is subsequently to be done with atoms removed from aworkpiece, such feedstock may be referred to as “waste atoms.” Feedstockmust be atomically-precise.

A “handle structure” comprises a plurality of atoms whose bondingpattern is not altered during a site-specific mechanosynthetic chemicalreaction and whose primary function is to hold a tip(s) or workpiece(s)to facilitate a mechanosynthetic chemical reaction when the handlestructure is manipulated by a positional device. Handle structure mayinclude the null case (e.g., a tip or workpiece bound directly to apositional means).

An “inert environment” includes, but is not limited to, ultra-highvacuum (UHV), argon, nitrogen, helium, neon, or other gases or liquids,either individually or in combination, that do not react with thetip(s), feedstock, or workpiece(s) during mechanosynthetic operations.

“Inverted mode”: see definition within “Conventional Mode” definition.

“Mechanical force” may include applied mechanical forces havingpositive, negative, or zero magnitude. Chemical reactions driven by theapplication of mechanical force include reactions that are (1) driventhrough its reaction barrier by mechanically forcing reactants orproducts through the transition state, or (2) driven away from anundesired reaction by mechanically restraining potentially reactivesites from attaining closer physical proximity, or (3) allowed to occurby bringing potentially reactive sites into closer physical proximitywhen zero mechanical force is required to do so, as for example when noreaction barrier exists, or when thermal energy alone is sufficient tosurmount the reaction barrier.

“Mechanosynthesis” is the use of positional control and mechanical forceto facilitate site-specific chemical reactions involved in the building,alteration, or disassembly of a workpiece. Mechanosynthesis does notrequire voltage biases, but neither does it exclude their use.

A “mechanosynthetic reaction” (sometimes referred to as a “reaction”when context makes it clear that the reaction is mechanosynthetic) is achemical reaction carried out using mechanosynthesis.

A “meta-tip” is a handle to which multiple tips are attached. Forexample, a meta-tip could be prepared using a conventional SPM probewith a flat surface on the end, which is then functionalized withmultiple tips.

A “modular tip” is a tip with a modular design. Modules include anactive site, a body, feedstock, legs, and linkers. Some of these modulesmay be considered to be modular themselves. For example, a body containsan active site, and the active site may be said to include feedstock.Similarly, linkers can be thought of as part of the leg module. Amodular tip may be referred to as simply a “tip” when context makes thetype of tip clear.

A “positional device” is a device capable of exerting atomically-precisepositional control on a mechanosynthetic tip, tool, or workpiece, andmay include, but is not limited to, scanning probe microscopes (SPM) andatomic force microscopes (AFM) and related devices, a miniaturized orMEMS-scale SPM or AFM, a robotic arm mechanism of any size scale, orother appropriate manipulation system capable of atomically-precisepositional control and appropriate force application. Many types of suchpositional devices are known to those skilled in the art, but forexample, actuators can be based upon piezo elements or electrostatics.Metrology based upon piezo elements, or optical (e.g., interferometry),capacitive, or inductive techniques, or other technology, can be usedfor positional feedback if required.

A “presentation surface” is a surface which can be used to bindfeedstock or tips for use in mechanosynthesis, and as a base on which tobuild a workpiece. Although generally monolithic, a presentation surfacecan be composed of more than one material (e.g., gold and silicon couldboth be used where each has advantageous aspects), or composed ofmultiple non-adjacent surfaces. A presentation surface may be referredto simply as a “surface” when context makes the meaning clear.Presentation surfaces include the appropriate area(s) on handlestructures and meta-tips. Presentation surfaces are preferably as closeas possible to atomically-flat, but this is largely a convenience havingto do with standard equipment design, and to facilitate higher speedsand reduced scanning (e.g., to create topological maps of non-flatsurfaces), rather than an absolute requirement.

“Site-specific” refers to a mechanosynthetic reaction taking place at alocation precise enough that the reaction takes place between specificatoms (e.g., as specified in a build sequence). The positional accuracyrequired to facilitate site-specific reactions with high reliability isgenerally sub-angstrom. With some reactions that involve large atoms, orthose with wide trajectory margins, positional uncertainty of about 0.3to 1 angstrom can suffice. More commonly, a positional uncertainty of nomore than about 0.2 angstroms is needed for high reliability. Somereactions, for example, due to steric issues, can require higheraccuracy, such as 0.1 angstroms. These are not hard cutoffs; rather, thegreater the positional uncertainty, the less reliable a reaction willbe.

A “structural atom” in an adamantane-like molecular structure refers toan atom comprising the cage framework, for example a carbon atom in anadamantane molecule. More generally, a structural atom is an atom thatcomprises part of the backbone or overall structure in a highly-bondedmolecule.

A “synthetic tip” is an atomically-precise tip manufactured via a bulkmethod, such as gas or solution-phase chemistry, rather than viamechanosynthesis. A synthetic tip be referred to as simply a “tip” whencontext makes the type of tip clear.

A “terminating atom” refers to an atom that does not serve as astructural atom but absorbs unused valences of a structural atom. Forexample, a hydrogen atom in an adamantane molecule.

A “three-dimensional” workpiece means a workpiece including a lattice ofatoms whose covalent structure occupies more than a single plane,discounting bond angles. Under this definition, for example, mostproteins (discounting e.g., disulfide inter- or intra-molecular bonds)and other polymers would be two dimensional, as would a plane ofgraphene. A covalent network solid or a carbon nanotube would bethree-dimensional.

A “tip” is a device for facilitating mechanosynthetic reactions whichincludes one or more “active” atoms or sites whose bonding pattern orelectronic state is altered during a mechanosynthetic operation, and oneor more “support” atoms whose bonding pattern or electronic state is notaltered during a mechanosynthetic operation. The support atoms hold theactive atoms in position, and may also modify the chemical behavior ofthe one or more active atoms. Unless otherwise specified, a tip isatomically-precise.

“Tip swapping” is the process of connecting a new tip and handlestructure to a positional means. In conventional SPM, this may be doneby, for example, manually changing the probe, or using equipment withprobe magazines which hold multiple probes and can automate tipswapping.

A “tool” comprises a tip, potentially bonded to a handle, controlled bya positional device or means.

A “workpiece” is an apparatus, article of manufacture, or composition ofmatter, built via mechanosynthesis. A system may have more than oneworkpiece. A workpiece may be connected to, but does not include,non-atomically-precise structures such as a support substrates orpre-existing structures onto which a workpiece is built.

Chemical Structure and Scientific Notation

A dot (“.”) is may be used in chemical structures herein to represent anelectron, as in the radical group “.CH2”. For ease of typesetting, thenotation herein generally omits subscript or non-standard characters.Superscript may be written using the “^” character when required forclarity.

Synthetic Tips

Previous literature described (see, e.g., U.S. Pat. No. 9,244,097 orWO2014/133529) a bootstrap process to facilitate the creation ofatomically-precise tips from atomically-imprecise tips usingmechanosynthesis. This is a potentially complex process, requiring thecharacterization of atomically-imprecise tips, to then performmechanosynthetic reactions with those tips, to build atomically-precisetips. Being able to skip this step is therefore quite useful. As analternate method of preparing atomically-precise tips, we describe thebulk synthetic chemical preparation (and if appropriate, passivation,and depassivation or activation) of various atomically-precise tips.

Bulk synthetic preparation of tips allow the avoidance of abootstrapping process. As will also been seen, bulk presentation of suchtips on a surface allows a fundamentally different way of dealing withfeedstock provisioning, waste atom disposal, and access to multipletips.

With respect to feedstock provisioning, previous work such asWO2014/133529 describes the use of feedstock depots and trash depots.Feedstock depots are presentation surfaces to which feedstock has beendirectly bound. Trash depots are surfaces which provide for wastedisposal by allowing a tip to transfer unwanted atoms from the tip tothe surface. One drawback to this method is the lack of chemicaldiversity available on the surface(s). On a uniform surface, differentfeedstock will have different affinity, potentially higher or lower thanoptimal. Herein we describe a way to completely avoid needing to bindfeedstock or waste atoms directly to a surface by using “tips on asurface.” In addition to using presentation surfaces directly asfeedstock and trash depots, previous proposals describe rechargeabletips, employing strategies that use a relatively small number of tipsover and over again during a build sequence. Herein we describe methodsfor partially or completely avoiding tip reuse, and hence we are able toomit tip recharge steps (e.g., as described in WO2014/133529),streamlining the entire process.

Synthetic tips, because they can be made via bulk chemistry techniques,are available in very large numbers after synthesis (like the moleculesin most bulk chemical reactions, “very large numbers” can mean up tomillions, billions, or even far more, ranging into numbers that requirescientific notation to easily express). Therefore, a large number ofsynthetic tips could be affixed to a presentation surface. The synthetictips can be pre-charged (meaning, the tips are already in the chemicalstate desired to carry out the intended reactions, such as already beingbonded to feedstock), and they can include large numbers of every typeof tip required for a given build sequence. In this way, thepresentation surface can serve purposes including being a feedstockdepot (the synthetic tips already being charged with their feedstock), atrash depot (e.g., radical tips could be used to bind waste atoms), anda varied collection of tips that can carry out all necessary reactions(for example, almost any number of tips, including all the tipsdescribed herein, or in previous work such as WO2014/133529, could bepresent on a presentation surface, and all in large numbers). Using alarge number of synthetic tips also allows each tip to be disposable,rather than requiring recharge for subsequent use, avoiding the need todesign and perform recharge operations.

The availability of large numbers of tips on a surface raises the ideathat a workpiece could be connected to a positional means, allowing theworkpiece to move to the tips (“inverted mode”), rather than tips movingto the workpiece (“conventional mode”). Conceptually, if the workpiecemoves and the presentation surface is stationary, one could think of abuild sequence as a workpiece moving around a presentation surface,aligning itself with a desired tip, and then being brought into contactwith that tip with sufficient force to trigger a mechanosyntheticreaction. The tip that was used is then spent, but the presentationsurface can easily provide large numbers of tips. The build sequenceproceeds by then aligning the workpiece with the next appropriateunspent tip and bringing them together. This process repeats until theentire workpiece is built.

Note that, as is discussed elsewhere herein, in some embodiments, theprocess of mechanosynthesis may involve scanning the presentationsurface to establish a topological map and the positions of the tips tobe used. If the tips have been mapped, software can be used to keeptrack of which locations have been used and which have not. Analternative implementation would be to simple scan for unused tips asthey are needed, since a used tip and an unused tip would have markedlydifferent characteristics when evaluated via, e.g., STM.

Other variations on this concept are also possible, including a toolwhich holds multiple tips (a “meta-tip”). Such designs may be moreefficient than a tool holding a single tip because multiple reactionscould be performed without requiring tip swapping or tip recharge.Whether the tips reside on a presentation surface, or on a tool, andwhether the presentation surface, the tool, the workpiece, or somecombination thereof are coupled to positional means, the overarchingpoint is a design which has at least some of the followingcharacteristics and advantages, among others.

First, a plurality of tips can be made available. These tips could beall the same, or could include many different types of tips. If multipletip types are present, they could be randomly intermingled, segregatedby sector or position, or the tips could be laid out in an order whichmaximizes the efficiency of a build sequence (for example, by arrangingdifferent tip sectors in a manner that minimizes the movement requiredto perform the mechanosynthetic operations to build a particularworkpiece, or considering a more general design, locating tips that areapt to be used more frequently closer to the workpiece, or locating tipsectors concentrically around a workpiece to minimize total tip toworkpiece distance regardless of the order of reactions).

Second, due to the large number of tips that are accessible to thesystem, tip recharge may be reduced or eliminated during a buildsequence. Each tip can be used once, and then ignored once it is spent.By eliminating recharge reactions, shorter, faster build sequences arefacilitated. If additional tips were still required, e.g., for aworkpiece requiring a number of tips beyond that which are available,the strategy of mounting a large number of tips, preferably in theirready-to-use state, on a surface, allows the bulk replacement of tips byswapping in a new surface. In this scenario, tip recharge is notcompletely eliminated, but it is greatly reduced.

Third, tips do not have to be swapped for chemical diversity becauseevery type of tip needed for a given build sequence can be presentsomewhere on the presentation surface. This reduces or eliminates theneed for multiple positional means or tip swapping.

Fourth, large numbers of atomically-precise tips can be prepared andaffixed via bulk chemical reactions (and bulk activated, if required).This eliminates the need for a bootstrap process that usesnon-atomically-precise tips to create atomically-precise tips. It alsoreduces or eliminates the need to build tips using mechanosynthesis,which can be useful where mechanosynthetic operations are the ratelimiting step of a manufacturing process. Exemplary synthetic pathwaysfor multiple synthetic tips are described herein.

Fifth, system complexity is kept relatively low, and the number of tipsand feedstock moieties available can be relatively high, as compared toother proposals for providing feedstock via, for example, methods whichrequire cartridges or conveyor belts (Rabani, “Practical method andmeans for mechanosynthesis and assembly of precise nanostructures andmaterials including diamond, programmable systems for performing same;devices and systems produced thereby, and applications thereof” UnitedStates. 2009. Ser. No. 12/070,489.).

With respect to the number of tips that may be available under some ofthese scenarios, this can vary greatly. For example, on a very smallsurface, such as a small flat at the end of a probe tip (which wouldtraditionally hold one tip and could do so in some embodiments of thepresent invention), small numbers of tips could be provided for chemicaldiversity. For example, two to ten tips could be placed on the end of aprobe, requiring no more than a few square nanometers of space. Thiswould provide convenient access to tips of varying chemical naturewithout needing to swap probes. Assuming a build sequence requiring morereactions than a small batch of tips like this can provide, such tipswould still have to be recharged, but the advantage is that this couldbe done chemically (e.g., by touching the tip to appropriate surfaces toabstract or donate feedstock) rather than requiring physical swapping ofan entire tip and handle.

On larger surfaces, much larger numbers of tips could be presented. Forexample, a presentation surface on the order of square nanometers couldprovide dozens, hundreds, or thousands of tips. A presentation surfaceon the order of square microns could provide room for millions orbillions of tips. And, if even larger numbers or greater space aredesired, long-distance metrology can allow presentation surfaces on theorder of square millimeters or centimeters while still maintaining therequisite positional accuracy. (Lawall, “Fabry-Perot metrology fordisplacements up to 50 mm,” J. Opt. Soc. Am. A. OSA. 2005. 22:2786-2798)

When using a plurality of tips, the tips could all be the same (helpingto reduce recharge reactions, as described herein), but as chemicaldiversity is also useful, there could also be almost any number ofdifferent types, from two different types, to the at least eight maintip/feedstock combinations described in, e.g., FIGS. 3-7 (or nineincluding the later-described AdamRad-Br tip), or even substantiallymore given the different types of linkers, feedstock, other tip designsthat could be used, and the potential desire for tips to facilitate newreactions or that would work under different conditions.

Surface-Mounted Tips

Synthetic tips, if properly designed, can be chemically bound to apresentation surface, or “surface-mounted.” In addition to beingamenable to synthesis using traditional chemistry, and carrying out oneor more mechanosynthetic reactions, surface-mounted tips are designed toallow efficient bonding to a presentation surface (often in largequantity).

Surface-mounted tips differ from the tips normally used in SPM work inthat they are not simply integral to a handle structure (e.g.,commercially available tips often have a tip where the crystal structureof the tip is contiguous with the handle structure; essentially the tipis just the end of the handle structure), nor are they a handlestructure to which only a trivial functionalization has been added(e.g., bonding a single CO molecule to the end of an existing tip is acommon technique to increase resolution). Surface-mounted tips differfrom previously-proposed mechanosynthetically-created tips in that theydo not require mechanosynthesis to manufacture (which has not onlyprocess implications, but structural and chemical implications sincethis requires that surface-mounted tips be able to bind to the desiredsurface without the aid of mechanosynthesis). Given this, whilesurface-mounted tips may appear superficially similar to other tipsdescribed in the literature, the requirements for the design of tipswhich are to be surface-mounted are substantially different.

Binding orientation is one issue that must be addressed when designingsurface-mounted tips. It would be preferable that the tips only affixthemselves to a surface in a manner that renders them properly orientedfor use in mechanosynthetic reactions (although multiple possibleorientations could be acceptable given the number of redundant tips thatcould be present—the system could scan to identify and use only tips inthe desired orientation, but this reduces efficiency).

Active sites and legs are discussed in more detail herein, but are majorfactors in ensuring that correct binding orientation is obtained. Forexample, tips with radical active sites will be highly reactive in theiractive form. Due to this high reactivity, the active site may bind tothe presentation surface instead of the legs. If this happens, the tipwould end up bound to the presentation surface upside down or at leastimproperly oriented. Reactive sites may also form bonds to other partsof the same tip, or may form bonds to other tips, such as two tipsdimerizing. This problem may be avoided in the case of reactive activesites by binding the tip to the presentation surface while the activesites are neutralized. The active sites can then be activated after legbinding. A similar issue presents itself with respect to the legs. Thelegs (or leg linkers) need to be reactive enough that they will bind tothe presentation surface, but they must resist pathological reactionswith themselves or other tips (e.g., forming a leg-leg bond instead of aleg-surface bond, or undergoing any other undesired reactions).

Of course, there are other design consideration for tips, including thatthey perform the desired reactions reliably during a build sequence, butthe above concerns are unique to bulk-synthesized, surface-mounted tips.Tips created using mechanosynthesis can largely avoid the problemsdescribed above via the positional specificity of the reactions used intheir synthesis.

Modular Tip Design

As will be seen in subsequent examples, surface-mounted tips can bethought of as being modular. Each tip can be thought of as having anactive site (one or more atoms that bind a desired atom or group ofatoms, which could be, e.g., feedstock for a donation reaction, or somemoiety to be removed from a workpiece for an abstraction reaction), abody (adamantane or an adamantane derivative in our examples, but otherstructures could be used given the teachings herein), and one or morelegs that serve to attach the tip to a surface. The feedstock of a tipcould also be considered a module, as could the surface, which, althoughnot technically part of the tip, can be important to tip design andfunction.

To aid in understanding how tips function, and how they can berationally designed, considerations pertinent to each module aredescribed below. Note that the specific examples presented useadamantane, or adamantane-like bodies. Many reactions forfunctionalizing adamantanes are known, and their stiffness, small size,computational tractability and other favorable characteristics lead usto use these structures as exemplary tips, although many differentmolecules, including other adamantane-like structures, could serve thesame purpose.

The active site's main characteristic is that it reliably facilitate thedesired reaction on a workpiece. However, how to efficiently synthesizeand deliver tips to a surface, and prepare them for use, must beconsidered in their design. Particularly when a tip's ready-to-use formincludes a radical, a tip may incorporate a protective cap (what insolution-phase chemistry is commonly referred to as a “protectinggroup”). This cap reduces the active site's reactivity prior to use toavoid, for example, tip-tip dimerization, binding of the active site tothe surface, or other undesired reactions. However, the cap must beremovable so that the tip can be activated for use. One way to do thisis to make the cap photo-cleavable, but other methods are possible andwell-known in the field of chemistry.

The body may contain, or serve as a point of attachment for, the activesite. The body also serves as a point of attachment for one or morelegs. The body can also serve to tune the active site, and to isolate itfrom other chemical influences. With respect to tuning the active site,for example, substitutions which alter bond lengths, angles, orelectronegativity may be used to increase or decrease the affinity ofthe active site for its feedstock. With respect to isolation, the bodyprovides chemical isolation from, for example, the legs. Such isolationis one of the aspects of this modular design paradigm that eases thedesign of new tips by allowing modules to be put togethercombinatorially. For example, if an active site and body combinationthat accomplish the desired reaction are already known, but one desiresto use a different surface which necessitates different legs, it islikely that the new legs can be swapped in without redesign of the bodyand active site. If the legs were connected directly to the active site,their chemical nature would tend to have more of an effect on the activesite, potentially requiring redesign of the body, or unnecessarilyconstraining the choice of legs. Another characteristic of the body isthat it is preferably rigid. A rigid body will tend to be more versatilebecause a rigid body will better resist deformation when forces areapplied to it during mechanosynthetic reactions.

The legs serve to attach the body to the surface. The legs preferablyhave a geometry that permits them to bind the body to a surface withoutexcessive strain, including surfaces that are functionalized prior toleg attachment. Functionalized surfaces, such as chlorinated Si, maymake longer legs preferable because the, e.g., Cl atoms, can be directlyunder the tip body, making some clearance between the body of the tipand Si surface preferable. Legs are also preferably fairly rigid, andstrong enough so that reactions require the application of force proceedreliably rather than the tip tilting, otherwise moving, or breaking aleg bond. While legs that are too short may be unable to bond to thesurface reliably, legs that are too long may be too flexible, adding tothe positional uncertainty of the tip atoms during a mechanosyntheticoperation. Where issues such as surface functionalization and latticemismatches between the surface and body are not issues, legs can be veryshort (e.g., a single oxygen atom could serve as each leg).

With respect to the number of legs, the examples provided depict tipswith three legs. Three legs helps provide stability against forcesacting upon the active site or feedstock at varied angles, and canreduce the force on any given leg by spreading it amongst all legs.However, tips with one or two legs could be used, as could tips withfour, or more, legs. Note that tips with more than one leg may be usablewhen not all of their legs have bound to the presentation surface, aslong as the required stability is provided. On a tip with multiple legs,each leg does not need to be identical.

Legs may incorporate linkers (if not, the leg may be considered to alsobe the linker, or vice versa), which serve to provide a bridge betweenthe rest of the leg and the body or surface. The advantage of linkers isin providing an appropriate chemistry with which to bind a surface. Forexample, if the rest of the leg does not have the necessary reactivityor bond strength with a surface, a linker may address the issue. This isdemonstrated with the exemplary tips described herein, wherein each tipmay have, e.g., a trifluorobenzene leg, and to that leg may be attacheda linker which is, e.g., NH, O, or S. This modular swapping of linkersallows otherwise-identical tips to be adapted to various surfaceswithout compromising the characteristics of the active site. Linkers mayalso be used to adjust the geometry of the legs, for example, helpingthem to fit the surface lattice spacing better, adjusting their length,or altering their rigidity.

Feedstock serves as a source of atoms which can be added to a workpieceand is generally attached to the “top” (with respect to the orientationdepicted in, e.g., FIG. 1-17, although the real-world orientation maydiffer) of the tip to provide access to the feedstock without stericinterference from other parts of the tip or the surface. Feedstock ischosen not only by what atom or atoms it contains, but by how it bindsto a tip's active site and the desired location on a workpiece. Thereare many ways, for example, to donate carbon atoms to a workpiece, andexamples using C2, CH2, and CH3 are all presented herein. Context willdetermine which is most appropriate, though often more than one could beused to build a given workpiece, assuming appropriate alterations in thebuild sequence.

The surface to which a tip is being attached has a variety of importantcharacteristics, including chemical reactivity, surface smoothness,lattice spacing, linker-surface bond strength, and internal bondstrength. In terms of chemical reactivity, the surface must bind to thelinkers during the tip binding process, but preferably not to otherparts of the tip. The surface's lattice spacing must allow linkerbinding without excessive strain. The linker-surface bond strength mustsuffice so that the bonds do not rupture if pulling forces are required.And, the internal (surface-surface) bonds must be of sufficient strengththat, if pulling forces are required, the entire tip, along with one ormore surface atoms, is not ripped from the surface.

With surface-mounted tips being broken down into the described modules,and the important functional characteristics of each module described,and realizing that this modular design at least to an extent isolatesvarious modules from one another, facilitating module re-use andcombinatorial creational of new tips, along with the examples presentedherein, this provides a design paradigm for the design and synthesis ofnew tips that can be generalized well beyond the specific examplesprovided.

FIG. 1 depicts one version of an abstraction tip that may be used toremove hydrogen, among other moieties, from a workpiece. Radical 101 isused to bind the moiety to be abstracted, and serves as the tip's activesite. The active site is connected to body 102, which in this example isadamantane. The body is connected to three methyl group legs,exemplified by leg 103. Each leg contains a sulfur linker, exemplifiedby linker 104. Each linker is bound to surface 105. As an abstractiontip being depicted in its ready-to-use state, no feedstock is present.

As a different example, with feedstock, FIG. 2 depicts one version of atip capable of donating hydrogen to many atom types. Active site 201 isa Ge atom, which in this case is part of a substituted adamantane body202. Trifluorobenzene (which could be viewed as trifluorophenol ifconsidered together with the linkers) legs are used, exemplified by leg203, and each leg is connected to an oxygen linker 204, which connectsto surface 205. Feedstock 206 is connected to active site 201.

Exemplary Tips

Surface-mounted tips, along with their routes of synthesis, have beendevised which carry out mechanosynthetic reactions while minimizing oreliminating issues such as tip dimerization and improper tip orientationduring surface mounting, and allow for proper leg length, flexibilityand linker chemistry to bind to the exemplary surfaces. These syntheticroutes allow for the bulk manufacture of many diverse tip types, therebyfacilitating many different mechanosynthetic reactions while having thebenefits described for surface-mounted tips and the processes for usingsuch tips.

The set of tips described includes an abstraction tip with a C2-basedactive site (capable of extracting many atoms from many different typesof workpieces, including, e.g., hydrogen from diamond), a hydrogendonation tip, a C2 donation tip, a Methyl donation tip, and a donationtip which can donate SiH3, GeH3, Si(CH3)3, or Ge(CH3)3, depending on thefeedstock attached to the Ge active atom in its substituted adamantanebody.

To demonstrate the modular design described herein, various versions ofeach tip are depicted. Specially, each tip is shown with threetrifluorobenzene legs which can be linked to either a chlorinatedsilicon surface, or a partially-hydrogenated partially-chlorinatedsilicon surface, via an oxygen linker or an NH linker. A version of eachtip is also depicted where the legs are methyl groups, using sulfurlinkers to connect to an Au surface. These various versions provide fora variety of surface properties and surface attachment chemistries anddemonstrate how a body can be used to isolate an active site from otherchanges in the tip, as the tips continue to function as desired afterchanging the legs, linkers, and surface.

Note that a silicon surface has stronger intra-surface bonds than a goldsurface. When placing tips on a gold surface, reactions that requiresubstantial pulling forces (exceeding a few nN) may pull the tip fromthe surface (taking one or more gold atoms with it), or cause the tip toslide sideways across the surface. Nonetheless, the thiol linkerchemistry is very accessible, making gold a useful surface (along withlead and other similar materials) if reactions with substantial pullingforces are not required.

Each exemplary tip is shown in detail, bonded to an appropriate surfacefor the linker chemistry depicted, in FIGS. 3-17. FIGS. 3-7 all depicttips that use trifluorobenezene legs and oxygen linkers on a siliconsurface. Specifically: FIG. 3 depicts an abstraction tip having aC2-radical-based active site, an adamantane body, trifluorobenzene legs,and oxygen linkers, on a silicon surface (all Si surfaces include, e.g.,chlorinated, partially-chlorinated, and partially-hydrogenated,partially-chlorinated Si). This tip will be referred to as AbstractionO.FIG. 4 depicts a hydrogen donation tip with hydrogen feedstock, aGe-based active site incorporated into a substituted adamantane body,trifluorobenzene legs, and oxygen linkers, on a silicon surface. Thistip will be referred to as HDonationO (or “HDonation,” omitting thespecific linker group, to denote any of the variants, a conventionalwhich can apply to any of the tip names). FIG. 5 depicts a C2 donationtip with .C2 feedstock, and otherwise the same structure as FIG. 4. Thistip will be referred to as C2DonationO. FIG. 6 depicts a methyl donationtip with .CH2 feedstock, and otherwise the same structure as FIG. 4.This tip will be referred to as MeDonationO. FIG. 7 depicts a donationtip that can be used to donate a variety of feedstock moieties dependingon the identity of the M and R groups. M can be Si or Ge, and R can be Hor CH3, allowing the tip to donate SiH3, GeH3, Si(CH3)3 or Ge(CH3)3.These tips will be referred to, respectively, as SiH3DonationO,GeH3DonationO, SiMe3DonationO, and GeMe3DonationO. FIG. 7 has otherwisethe same structure as FIG. 4.

FIGS. 8-12 depict tips with the same feedstock (if present), activesite, bodies, and legs as FIGS. 3-7, respectively, but each tip in FIGS.8-12 uses NH linkers instead of oxygen linkers to connect to a siliconsurface. These tips will be referred to, respectively, as AbstractionNH,HDonationNH, C2DonationNH, MeDonationNH, and for the various versions ofFIG. 12, SiH3DonationNH, GeH3DonationNH, SiMe3DonationNH, andGeMe3DonationNH.

FIGS. 13-17 depict tips with the same feedstock (if present), activesite, and bodies as FIGS. 3-7, respectively, but each tip in FIGS. 13-17uses methyl legs and a sulfur linker to connect the tip to a goldsurface. These tips will be referred to, respectively, as AbstractionS,HDonationS, C2DonationS, MeDonationS, and for the various versions ofFIG. 17, SiH3DonationS, GeH3DonationS, SiMe3DonationS, andGeMe3DonationS.

In addition to the use of these tips in their charged state, some tipscould be used in their uncharged state. For example, several of thetips, such as the hydrogen donation tip, have a Ge radical active sitein their discharged state. This can be a useful form of these tips, forexample, to break into a C═C bond, or as a trash depot for unwantedatoms (assuming appropriate affinity).

With respect to naming conventions, note that sometimes tips aredescribed in terms of what reaction they perform, and sometimes in termsof their structure and payload. For example “MeDonation” (regardless ofwhether the tip's legs are based on NH, O, S, phenylpropargyl alcohol,or something else) stands for “methyl donation” since that is what thetip does. With respect to naming via structure and payload, for example,many of the donation tips described herein have Ge-substitutedadamantane bodies. With no feedstock, the Ge atom would be a radical,and so may be referred to as “GeRad.” Similarly, “AdamRad” is anadamantane molecule without the C to Ge substitution, but rather havinga radical carbon at the active site. An adamantane can also besubstituted with a silicon atom at its active site, which may be calledSiRad. Obviously, these are just examples used to describe namingconventions, not a list of all possible structures or substitutions,which are numerous. To convey what feedstock is attached, the names maybe written as, for example, GeRad-CH2 (which is one implementation of anMeDonation tip), GeRad-H (one implementation of an HDonation tip).Understanding these conventions, the tip name normally makes itsstructure and/or function obvious.

Tip Synthesis

Exemplary synthetic pathways for each tip are depicted in FIGS. 18-41.Note that multiple synthetic pathways for the tip depicted in FIGS. 7,12 and 17 due to the various possible combinations of M and R. Tips withradicals in their active form are synthesized with a protective cap.Procedures for cap removal are described herein.

FIG. 18 depicts a synthetic pathway for AbstractionO. The synthesissteps are as follows: Commercially available 1,3,5-trihydroxyadamantanereacts with 2,4,6-trifluorophenol while heated between 50-80° C. underacidic conditions to give OFA-1. Treating OFA-1 with an excessdimethyldioxirane (DMDO) in acetone at room temperature selectivelyoxidizes the tertiary C—H bond to give alcohol OFA-2. Using Koch-Haafconditions (Stetter, H., Schwarz, M., Hirschhorn, A. Chem. Ber. 1959,92, 1629-1635), CO is formed from the dehydration of formic acid byconcentrated sulfuric acid between −5-0° C. The CO forms a bond with thetertiary carbocation formed from the dehydration of the bridgeheadalcohol at room temperature. Upon aqueous workup the carboxylic acidOFA-3 is obtained. Esterification of the carboxylic acid OFA-3 with drymethanol and catalytic sulfuric acid between 40-60° C. yields the methylester OFA-4. The phenolic —OH groups in OFA-4 are protected withtert-butyldimethylsilyl chloride (TBSCl) in the presence of imidazole atroom temperature to give the TBS-silyl ether OFA-5. Reduction of themethyl ester with LiAlH4 in tetrahydrofuran (THF) between 0° C. and roomtemperature gives the methyl alcohol OFA-6. Oxidation of the methylalcohol to the aldehyde OFA-7 proceeds with catalytictetrapropylammonium perruthenate ((Pr4N)RuO4, TPAP) and stoichiometricN-methylmorpholine-N-oxide (NMO). The presence of 4 Å powdered molecularsieves in the reaction mixture adsorbs any water present and decreasesthe probability of over-oxidation to the carboxylic acid (Ley, S. V.,Norman, J., Griffith, W. P., Marsden, S. P., Synthesis, 1994, 639-666).Using a modified Corey-Fuchs procedure (Michel, P., Rassat, A.Tetrahedron Lett. 1999, 40, 8570-8581), the aldehyde in THF is added toa premixed solution of iodoform (CHI3), triphenylphosphine, andpotassium tert-butoxide at room temperature in THF to undergo acarbon-carbon bond forming reaction to give the 1,1-diiodoalkene. Singleelimination of the vinyl iodide with excess potassium tert-butoxide andcareful temperature control (−78° C.-−50° C.) yields the iodoalkyneOFA-8. It is possible to form the terminal alkyne from this reaction iftemperature is not carefully controlled, however, the terminal alkynecan be iodinated with N-iodosuccinimide/AgNO3 or, alternatively, with I2in basic methanol. The final global deprotection of the TBS-silyl ethergroups is performed with tetra-n-butylammonium fluoride (TBAF). Uponaqueous workup, the AbstractionO tip with free phenol linkers OFA-9 isobtained.

FIG. 19 depicts a synthetic pathway for HDonationO. The synthesis stepsare as follows: FHD-104X is reduced by excess lithium aluminum hydridein THF solvent at 0° C., converting the germanium halide to thegermanium hydride FHD-105. Tetra-n-butylammonium fluoride is used todeprotect the tert-butyldimethylsilyl protecting groups from FHD-105 inTHF to yield the triphenol FHD-106, the HdonationOHtip.

FIG. 20 depicts a synthetic pathway for C2DonationO. The synthesis stepsare as follows: The Grignard reagent ethynylmagnesium bromide in THFsolution is added to FHD-104X dissolved in dry THF and cooled to −78 Cdropwise with rapid stirring. The reaction is stirred for 1 hour, warmedto 0 C for 1 hour, and stirred for 1 hour at room temperature to formFC2D-101. FC2D-101 is dissolved in dry THF and cooled to −78 C. Asolution of n-butyllithium in hexanes is added and the reaction isstirred for 1 hour at −78 C. A solution of iodine in dry THF is addedand the reaction is allowed to warm to room temperature to yieldFC2D-102. FC2D-102 is dissolved in THF and stirred rapidly at roomtemperature. Tetra-n-butylammonium fluoride is added and the reaction isstirred for 1 hour to yield FC2D-103, the C2DonationO tip.

FIG. 21 depicts a synthetic pathway for MeDonationO. The synthesis stepsare as follows: The germanium halide FHD-104X in THF solution is reducedwith lithium metal to generate a lithiated germanium species in situ.The solution is then slowly added dropwise to a solution of 10-foldexcess methylene iodide (CH2I2) in THF cooled to 0 C. This method ofaddition favors the formation iodomethyl germane FMeD-101 overmethylene-bridged germanes. Stoichiometric tetra-n-butylammoniumfluoride is used to deprotect the tert-butyldimethylsilyl protectinggroups from FMeD-101 in THF to yield the triphenol FMeD-102, theMeDonationO tip.

FIG. 22 depicts a synthetic pathway for SiH3DonationO. The synthesissteps are as follows: The phenols of FHD-106 are acylated with mesitoylchloride in dichloromethane with pyridine base. (Corey et al., JACS1969, 91, 4398) The mesitoate protecting group is utilized due to itsstability to the lithiation conditions necessary for FSiHD-102.FSiHD-101 in dry THF solution is deprotonated with n-butyllithium inhexanes at −78 C and slowly warmed to room temperature. The resultinglithiated anion is silylated with chlorotriethoxysilane in THF solutionto yield FSiHD-102. FSiHD-102 in dry THF solution is cooled to 0 C andlithium aluminum hydride in THF solution is added to cleave themesitoate esters and reduce the triethoxysilyl group, yieldingFSiHD-103, the SiH3DonationO tip.

FIG. 23 depicts a synthetic pathway for GeH3DonationO. The synthesissteps are as follows: To form FGeHD-101, the germanium halide FHD-104Xin THF solution is reduced with lithium metal to generate a lithiatedgermanium species in situ. The solution is then removed by syringe toseparate the lithiated germanium species from the unreacted lithiummetal and then slowly added dropwise to a solution ofchloro(phenyl)germane (Ohshita, J.; Toyoshima, Y.; Iwata, A.; Tang, H.;Kunai, A. Chem. Lett. 2001, 886-887) in THF cooled to 0 C. It isnecessary to separate the lithiated germanium species from excesslithium metal before addition to the trimethylgermanium chloride becauselithium is capable of exchange reactions with germanium halides.FGeHD-101 is dephenylated with trifluoromethanesufonic acid indichloromethane at 0 C. The crude reaction isolate after neutralizationand workup is then dissolved in dry THF. The reaction is cooled to 0 Cand lithium aluminum hydride is added dropwise to produce the germaneFGeHD-102, the GeH3DonationO tip.

FIG. 24 depicts a synthetic pathway for SiMe3DonationO. The synthesissteps are as follows: To prepare FSiHD-101, the phenols of FHD-106 areacylated with mesitoyl chloride in dichloromethane with pyridine base.(Corey et al., JACS 1969, 91, 4398) The mesitoate protecting group isutilitized due to its stability to the lithiation conditions necessaryfor FSiHD-102. FSiHD-101 in dry THF solution is deprotonated withn-butyllithium in hexanes at −78 C and slowly warmed to roomtemperature. The resulting lithiated anion is silylated withtrimethylsilyl chloride in THF solution to yield FSiMeD-102. FSiMeD-102in dry THF solution is cooled to 0 C and lithium aluminum hydride in THFsolution is added to cleave the mesitoate esters, yielding FSiMeD-103,the SiMe3DonationO tip.

FIG. 25 depicts a synthetic pathway for GeMe3DonationO. The synthesissteps are as follows: To prepare FGeMeD-101, the germanium halideFHD-104X in THF solution is reduced with lithium metal to generate alithiated germanium species in situ. The solution is then removed bysyringe to separate the lithiated germanium species from the unreactedlithium metal and then slowly added dropwise to a solution oftrimethylgermanium chloride in THF cooled to 0 C. It is necessary toseparate the lithiated germanium species from excess lithium metalbefore addition to the trimethylgermanium chloride because lithium iscapable of exchange reactions with germanium halides. Stoichiometrictetra-n-butylammonium fluoride is used to deprotect thetert-butyldimethylsilyl protecting groups from FMeD-101 in THF to yieldthe triphenol FGeMeD-102, the GeMe3DonationO tip.

FIG. 26 depicts a synthetic pathway for AbstractionNH. The synthesissteps are as follows: Commercially available 1,3,5-trihydroxyadamantanereacts with 2,4,6-trifluoroaniline while heated to 50-80° C. underacidic conditions in 1,2-dichloroethane to give NFA-1. Treating NFA-1tetrafluoroboric acid forms the tetrafluoroborate amine salt in situ toprevent oxidation of the amines. (Asencio, G., Gonzalez-Nunez, M. E.,Bernardini, C. B., Mello, R., Adam, W. J. Am. Chem. Soc., 1993, 115,7250-7253) Following the salt formation, an excess of dimethyldioxirane(DMDO) in acetone at room temperature selectively oxidizes the tertiaryC—H bond to give alcohol NFA-2. Using Koch-Haaf conditions (Stetter, H.,Schwarz, M., Hirschhorn, A. Chem. Ber. 1959, 92, 1629-1635), CO isformed from the dehydration of formic acid by concentrated sulfuricacid. The CO forms a bond with the tertiary carbocation formed from thedehydration of the bridgehead alcohol. Upon aqueous workup thecarboxylic acid NFA-3 is obtained. Esterification of NFA-3 with drymethanol and catalytic sulfuric acid yields the ester NFA-4 that can bereduced readily with diisobutylaluminum hydride.Di-tert-butyl-dicarbonate (Boc2O) is used to protect the —NH2 groups andto be removable by acid hydrolysis. Treating NFA-4 with Boc2O yields theprotected compound NFA-5. Reduction of the methyl ester with LiAlH4 intetrahydrofuran (THF) gives the methyl alcohol NFA-6. Oxidation of themethyl alcohol to the aldehyde NFA-7 proceeds with catalytictetrapropylammonium perruthenate (TPAP) and stoichiometricN-methylmorpholine-N-oxide (NMO). The presence of 4 Å powdered molecularsieves in the reaction mixture adsorbs any water present and decreasesthe probability of over-oxidation to the carboxylic acid. (Ley, S. V.,Norman, J., Griffith, W. P., Marsden, S. P., Synthesis, 1994, 639-666)Using a modified Corey-Fuchs procedure (Michel, P., Rassat, A.Tetrahedron Lett. 1999, 40, 8570-8581), the aldehyde in THF is added toa premixed solution of iodoform (CHI3), triphenylphosphine, andpotassium tert-butoxide at room temperature in THF to undergo acarbon-carbon bond forming reaction to give the 1,1-diiodoalkene. Singleelimination of iodide with careful temperature (−78° to −50° C.) andexcess potassium tert-butoxide control yields the iodoalkyne NFA-8. Itis possible to form the terminal alkyne from this reaction iftemperature is not carefully controlled, however, the terminal alkynecan be iodinated with N-iodosuccinimide/AgNO3 or, alternatively, with I2in basic methanol. The final global deprotection of the Boc-groups isperformed with trifluoroacetic acid (TFA) in dichloromethane at RT. Uponaqueous workup, NFA-9, the AbstractionNH tip, is obtained.

FIG. 27 depicts a synthetic pathway for HDonationNH. The synthesis stepsare as follows: NHD-103X in dry THF solution is cooled to 0 C andlithium aluminum hydride in THF solution is added to reduce thegermanium halide, yielding NHD-104. NHD-104 is dissolved in dry MeOH andadded to a reaction vessel suitable for pressurized hydrogenations.Palladium hydroxide catalyst is added and the vessel pressurized withhydrogen gas. Agitation of the reaction under the pressurized hydrogenatmosphere yields NHD-105, the HDonationNH tip.

FIG. 28 depicts a synthetic pathway for C2DonationNH. The synthesissteps are as follows: (Triisopropylsilyl)acetylene is dissolved in dryTHF and cooled to −78 C. n-Butyllithium solution in hexanes is slowlyadded dropwise to deprotonate the acetylene hydrogen. The solution isstirred for 1 hour, allowed to warm to room temperature, and is addeddropwise to NHD-103X in dry THF solution cooled to −78 C. The reactionis stirred for 1 hour, warmed to 0 C for 1 hour, and stirred for 1 hourat room temperature to form NC2D-101. NC2D-101 is dissolved in dry MeOHand added to a reaction vessel suitable for pressurized hydrogenations.Palladium hydroxide catalyst is added and the vessel pressurized withhydrogen gas. Agitation of the reaction under the pressurized hydrogenatmosphere yields NC2D-102. The steric bulk of both thetriisopropylsilyl group and the germaadamantane core preventhydrogenation of the alkyne. NC2D-102 is dissolved in THF and stirredrapidly at room temperature. Tetra-n-butylammonium fluoride is added andthe reaction is stirred for 1 hour at RT to yield NC2D-103. NC2D-103 isdissolved in MeOH and rapidly stirred. Potassium hydroxide is added anda solution of iodine in methanol is added slowly dropwise at RT to yieldNC2D-104, the C2DonationNH tip.

FIG. 29 depicts a synthetic pathway for MeDonationNH. The synthesissteps are as follows: The germanium halide NHD-103X in THF solution isreduced with lithium metal to generate a lithiated germanium species insitu. The solution is then slowly added dropwise to a solution of10-fold excess methylene iodine (CH2I2) in THF cooled to 0 C. Thismethod of addition favors the formation iodomethyl germane NMeD-101 overmethylene-bridged germanes. NMeD-101 is dissolved in dry MeOH and addedto a reaction vessel suitable for pressurized hydrogenations. Palladiumhydroxide catalyst is added and the vessel pressurized with hydrogengas. Agitation of the reaction under the pressurized hydrogen atmosphereyields NMeD-102, the MeDonationNH tip.

FIG. 30 depicts a synthetic pathway for SiH3DonationNH. The synthesissteps are as follows: The germanium halide NHD-103X in THF solution isreduced with lithium metal at −78 C to generate a lithiated germaniumspecies in situ. The solution is then removed by syringe to separate thelithiated germanium species from the unreacted lithium metal and thenslowly added dropwise to a solution of excess chlorotriethoxysilane inTHF cooled to 0 C and the reaction is allowed to warm to roomtemperature to produce NSiHD-101. NSiHD-101 in THF solution cooled to 0C is reduced with lithium aluminum hydride to generate NSiHD-102.NSiHD-102 is dissolved in cyclohexane and added to a reaction vesselsuitable for pressurized hydrogenations. Palladium hydroxide catalyst isadded and the vessel pressurized with hydrogen gas. Agitation of thereaction under the pressurized hydrogen atmosphere yields NSiHD-103, theSiH3DonationNH tip.

FIG. 31 depicts a synthetic pathway for GeH3DonationNH. The synthesissteps are as follows: The germanium halide NHD-103X in THF solution isreduced with lithium metal at −78 C to generate a lithiated germaniumspecies in situ. The solution is then removed by syringe to separate thelithiated germanium species from the unreacted lithium metal and thenslowly added dropwise to a solution of chloro(phenyl)germane in THFcooled to 0 C and the reaction is allowed to warm to room temperature toproduce NGeHD-101. It is necessary to separate the lithiated germaniumspecies from excess lithium metal before addition to thetrimethylgermanium chloride to prevent lithium-halogen exchangereactivity with the chloro(phenyl)germane. NGeHD-101 is dephenylatedwith trifluoromethanesufonic acid at 0 C. The crude reaction isolateafter neutralization of acid and workup is then dissolved in dry THF.The reaction is cooled to 0 C and lithium aluminum hydride is added toproduce the germane NGeHD-102. NGeHD-102 is dissolved in cyclohexane andadded to a reaction vessel suitable for pressurized hydrogenations.Palladium hydroxide catalyst is added and the vessel pressurized withhydrogen gas. Agitation of the reaction under the pressurized hydrogenatmosphere yields NGeHD-103, the GeH3DonationNH tip.

FIG. 32 depicts a synthetic pathway for SiMe3DonationNH. The synthesissteps are as follows: The germanium halide NHD-103X in THF solution isreduced with lithium metal at −78 C to generate a lithiated germaniumspecies in situ. The solution is then removed by syringe to separate thelithiated germanium species from the unreacted lithium metal and thenslowly added dropwise to a solution of excess chlorotrimethylsilane inTHF cooled to 0 C and the reaction is allowed to warm to roomtemperature to produce NSiMeD-101. NSiMeD-101 is dissolved incyclohexane and added to a reaction vessel suitable for pressurizedhydrogenations. Palladium hydroxide catalyst is added and the vesselpressurized with hydrogen gas. Agitation of the reaction under thepressurized hydrogen atmosphere yields NSiMeD-102, the SiMe3DonationNHtip.

FIG. 33 depicts a synthetic pathway for GeMe3DonationNH. The synthesissteps are as follows: The germanium halide NHD-103X in THF solution isreduced with lithium metal at −78 C to generate a lithiated germaniumspecies in situ. The solution is then removed by syringe to separate thelithiated germanium species from the unreacted lithium metal and thenslowly added dropwise to a solution of trimethylgermanium chloride inTHF cooled to 0 C and the reaction is allowed to warm to roomtemperature to produce NGeMeD-101. It is necessary to separate thelithiated germanium species from excess lithium metal before addition tothe trimethylgermanium chloride to prevent lithium reduction of thegermanium chloride. NGeMeD-101 is dissolved in cyclohexane and added toa reaction vessel suitable for pressurized hydrogenations. Palladiumhydroxide catalyst is added and the vessel pressurized with hydrogengas. Agitation of the reaction under the pressurized hydrogen atmosphereyields NGeMeD-102, the GeMe3DonationNH tip.

FIG. 34 depicts a synthetic pathway for AbstractionS. The synthesissteps are as follows: Commercially available 1-bromoadamantane undergoesa Friedel-Crafts alkylation with three separate benzene molecules underLewis acidic conditions with AlCl3 at 90 C to yield SHA-1. Carefulcontrol of the stoichiometry of the tert-butyl bromide (2.0 equivalents)yields the 1,3,5-triphenyl adamantane (Newman, H. Synthesis, 1972, 12,692-693). Treatment of SHA-1 in fluorobenzene and 50% aqueous NaOHsolution with a phase transfer catalyst gives SHA-2. This reaction isselective at brominating the tertiary C—H bond in the adamantane(Schreiner, P. R.; Lauenstein, O.; Butova, E. D.; Gunchenko, P. A.;Kolomitsin, I. V.; Wittkopp, A.; Feder, G.; Fokin, A. A., Chem. Eur. J.2001, 7, 4996-5003). Oxidative cleavage of the aromatic rings by RuCl3in a biphasic mixture gives the tricarboxylic acid SHA-3 (Carlsen, P. H.J.; Katsuki, T.; Martin, V. S.; Sharpless, K. B., J. Org. Chem. 1981,46, 3936-3938). Esterification of SHA-3 with dry methanol and catalyticsulfuric acid between 50-60° C. yields the triester SHA-4 that can bereduced readily with LiAlH4 at 0 C. The triol SHA-4 can react readilywith triflic anhydride and pyridine in dichloromethane at 0 C to givethe compound SHA-5. Condensing vinyl bromide at −20° C. with catalyticAlBr3 in the presence of the adamantyl bromide SHA-5 gives adibromoethyladamantane intermediate that is used with potassiumtert-butoxide to eliminate to give the alkyne SHA-6 (Malik, A. A.;Archibald, T. G.; Baum, K.; Unroe, M. R., J. Polymer Sci. Part A:Polymer Chem. 1992, 30, 1747-1754). Three equivalents of potassiumthioacetate displaces the triflate groups in refluxing acetonitrile togive the compound SHA-7. The use of 18-crown-6 enhances thenucleophilicity of the thioacetate and can be added to enhance the rateof the reaction at room temperature (Kitagawa, T., Idomoto, Y.;Matsubara, H.; Hobara, D.; Kakiuchi, T.; Okazaki, T.; Komatsu, K., J.Org. Chem. 2006, 71, 1362-1369). Silver nitrate with N-iodosuccinimidein THF creates the iodoalkyne at room temperature and treatment withpotassium hydroxide removes the acetate groups to give compound SHA-8,the AbstractionS tip.

FIG. 35 depicts a synthetic pathway for HDonationS. The synthesis stepsare as follows: Allowing RHD-101 to react with benzene andtrifluoroacetic acid (TFA) at room temperature in dichloromethane formsthe triphenylgermaadamantane SHD-101. Oxidative cleavage of the phenylgroups with catalytic RuCl3 in a solvent mixture of CCl4, CH3CN, and H2Owith periodic acid added as stoichiometric oxidant cleaves the aromaticrings between 0° C. to room temperature gives the tricarboxylic acidSHD-102. Esterification of SHD-102 with methanol with sulfuric acidbetween 40-60° C. gives the triester that can subsequently be reducedwith LiAlH4 at 0° C. to give the triol SHD-103. Triol SHD-103 can betreated with triflic anhydride at 0° C. with pyridine in dichloromethaneto give the triflate SHD-104. Displacement of the triflate groups withpotassium thioacetate in the presence of 18-crown-6 ether inacetonitrile at room temperature yields the acetate-protected thiols inSHD-105. Treatment of SHD-105 with a Lewis acid source including to butnot limited to SnCl4, I2, or Br2 in dichloromethane at −78° C. to roomtemperature selectively cleaves the Ge-Me bond to give the respectiveGe—X (X═Cl, Br, I) bond in SHD-106X. Treating the resulting Ge—Xcompound SHD-106X with LiAlH4 at 0° C. to room temperature reduces theGe—X bond as well as simultaneously removing the thioacetate groups fromthe thiols to yield the trithiol SHD-107, the HDonationS tip, uponaqueous workup.

FIG. 36 depicts a synthetic pathway for C2DonationS. The synthesis stepsare as follows: The intermediate SHD-106X from the HDonationS synthesisis allowed to react with an excess of commercially availableethynylmagnesium bromide solution in diethyl ether at 0° C. to roomtemperature to form SC2D-101. The excess of the ethynylmagnesium bromideensures full deprotection of the thioacetate protective groups uponaqueous workup. The thiols in SC2D-101 are protected with acetate groupsby treating it with acetic anhydride (Ac2O). The protected compound isthen treated with silver nitrate and a slight excess ofN-iodosuccinimide in THF at room temperature to form the iodoalkyne inSC2D-102. Subsequent treatment of the crude reaction mixture in basicmethanol at room temperature yields SC2D-102, the C2DonationS tip.

FIG. 37 depicts a synthetic pathway for MeDonationS. The synthesis stepsare as follows: The synthesis of the thiol methyl donation tool beginsfrom intermediate SHD-105. The acetate groups must be exchanged with athioether protective group, specifically the tert-butyl group, towithstand the synthetic conditions. The acetate groups are removed inbasic methanol at room temperature and then subsequently treated with anacidic solution of tert-butanol at room temperature to form SMeD-101.The Ge-Me bond is cleaved with a Lewis acid between −78° C. and roomtemperature with a reagent such as SnCl4, I2, or Br2 to yield the Ge—Clbond in SMeD-102X. Treating SMeD-102X with lithium metal and excessCH2I2 at 0 C in THF at high dilution yields SMeD-103. Removal of thetert-butyl groups is performed with 2-nitrobenzenesulfenyl chloride inacetic acid and yields a mixed disulfide (Pastuszak, J. J., Chimiak, A.,J. Org. Chem., 1981, 46, 1868. Quintela, J. M., Peinador, C.,Tetrahedron, 1996, 52, 10497). Treating this disulfide with NaBH4 at lowtemperature between −20° C. and 0° C. allows the recovery of the freethiol SMeDon-104, the MeDonationS tip, without reducing the C—I bond.

FIG. 38 depicts a synthetic pathway for SiH3DonationS. The synthesissteps are as follows: Intermediate SMeD-102X with t-butyl protectedthiols is treated with lithium metal in THF at 0° C. followed by theaddition of triethoxychlorosilane to give SSiHD-101 upon workup. Thisreaction forms the Ge—Si bond necessary for the SiH3 donor. The removalof the t-butyl groups is performed with the reagent2-nitrobenzenesulfenyl chloride in acetic acid at room temperature togive the mixed disulfide. Treatment with LiAlH4 cleaves the S—S bonds togive the free thiols in SSiHD-102, the SiH3DonationS tip, as well assimultaneously reducing the triethoxysilyl group to —SiH3.

FIG. 39 depicts a synthetic pathway for GeH3DonationS. The synthesissteps are as follows: Intermediate SMeD-102X with t-butyl protectedthiols is treated with lithium metal in THF at −78° C. The solution isthen removed by syringe to separate the lithiated germanium species fromthe unreacted lithium metal and then slowly added dropwise to a solutionof PhGeH2Cl at 0° C. to give SGeHD-101 upon workup. This reaction formsthe Ge—Ge bond necessary for the —GeH3 donor. Treatment of SGeHD-101with triflic acid cleaves the Ph-Ge bond to form a Ge—OSO2CF3 bond.Triflic acid also removes of the t-butyl thioether groups. Treatment ofthe this intermediate with LiAlH4 in diethyl ether at 0° C. cleaves anyS—S bonds to give the free thiols in SGeHD-102, the GeH3DonationS tip,as well as simultaneously reducing the Ge triflate group to —GeH3.

FIG. 40 depicts a synthetic pathway for SiMe3DonationS. The synthesissteps are as follows: Intermediate SMeD-102X with t-butyl protectedthiols is treated with lithium metal in THF at −78 C followed by theaddition of chlorotrimethylsilane upon warming to 0° C. Upon workup thecompound SSiMeD-101 with the Ge—Si bond is obtained. The removal of thet-butyl groups is performed with the reagent 2-nitrobenzenesulfenylchloride in acetic acid at room temperature to give the mixed disulfide.Treatment with NaBH4 in chloroform and methanol at room temperaturecleaves the S—S bonds to give the free thiols in SSiMeD-102, theSiMe3DonationS tip.

FIG. 41 depicts a synthetic pathway for GeMe3DonationS. The synthesissteps are as follows: Intermediate SMeD-102X with t-butyl protectedthiols is treated with lithium metal in THF at −78 C. The solution isthen removed by syringe to separate the lithiated germanium species fromthe unreacted lithium metal and then slowly added dropwise to a solutionof chlorotrimethylgermane at 0 C. Upon workup the compound SGeMeD-101with the Ge—Ge bond is obtained. The removal of the t-butyl groups isperformed with the reagent 2-nitrobenzenesulfenyl chloride in aceticacid at room temperature to give the mixed disulfide. Treatment withNaBH4 in chloroform and methanol at room temperature cleaves the S—Sbonds to give the free thiols in SGeMeD-102, the GeMe3DonationS tip.

FIG. 42 depicts a synthetic pathway for intermediate FHD-104X, fromwhich some of the other syntheses begin. The synthesis steps are asfollows: Cis, cis-Tri-O-alkyl 1,3,5-Cyclohexanetricarboxylate is reducedwith lithium aluminum hydride in refluxing THF and vigorous mechanicalstirring to yield cis, cis-1,3,5-tris(hydroxymethyl)cyclohexane HD-1.The procedure used resembles that found in Boudjouk et al.,Organometallics 1983, 2, 336. Cis,cis-1,3,5-Tris(hydroxymethyl)cyclohexane, HD-1, is brominated utilizingtriphenylphosphine dibromide generated in situ. This is accomplished byslow addition of bromine to a solution of the triol andtriphenylphosphine in DMF at room temperature to yield cis,cis-1,3,5-tris(bromomethyl)cyclohexane, HD-2. The procedure usedresembles that found in Boudjouk et al., Organometallics 1983, 2, 336.The tri-Grignard is generated in situ by adding cis,cis-1,3,5-Tris(bromomethyl)cyclohexane, HD-2, at room temperature tomagnesium turnings in THF and heating to reflux. The tri-Grignard isthen transferred to a second reaction vessel to separate the reagentfrom the excess magnesium turnings (Mg is capable of inserting into aGe—Cl bond). Trimethylchlorogermane, previously dried over calciumhydride and degassed, is added slowly dropwise to the reaction at 0 C.After 2 hours, the reaction is warmed to room temperature for two hours,and finally refluxed overnight. The reaction yields predominantly cis,cis-1,3,5-Tris(trimethylgermylmethyl)cyclohexane, HD-3. Cis,cis-1,3-dimethyl-5-(trimethylgermylmethyl)cyclohexane and cis,cis-1-methyl-3,5-bis(trimethylgermylmethyl)cyclohexane are also producedin small amounts. The procedure used is similar to that found inBoudjouk and Kapfer, Journal of Organometallic Chemistry, 1983, 296,339. HD-3 in benzene solution is subjected to redistribution reactionconditions using high purity anhydrous aluminum trichloride and heatingto reflux to yield 1-methyl-1-germaadamantane. HD-3 side products cis,cis-1,3-dimethyl-5-(trimethylgermylmethyl)cyclohexane and cis,cis-1-methyl-3,5-bis(trimethylgermylmethyl)cyclohexane may also bepresent in the reaction or isolated and reacted under these conditionsto yield HD-4 as well. HD-4 is reacted with excess “ketone free”dimethyldioxirane (DMDO) (Crandall, J. K. 2005. Dimethyldioxirane.e-EROS Encyclopedia of Reagents for Organic Synthesis.) in methylenechloride solution at −20 C to yield1-methyl-3,5,7-trihydroxy-1-germaadamantane RHD-101. The absence ofacetone in the reaction conditions allows for RHD-101 to precipitatefrom the reaction mixture, preventing over-oxidation. Upon completion ofthe reaction, isopropyl alcohol is used to quench the excess DMDO,preventing over-oxidation by excess reagent during reaction workup.RHD-101 is subjected to strongly acidic conditions in the presence of2,4,6-trifluorophenol at room temperature to yield FHD-102. The use ofBrønsted acidic conditions favors carbocation formation at the 3,5,7bridgehead positions of the adamantane cage structure overredistribution reactivity at the germanium center. The 1-methyl group ofFHD-102 can be exchanged with a halide (X═F, Cl, Br, I) with a varietyof electrophilic reagents at low temperatures ranging from −78 C up toroom temperature, depending on the halide desired. Reagents include, butare not limited to: Lewis acids such as SnCl4 or GaCl3, elementalhalides Br2 and I2 with Lewis acid catalyst, alkyl halides such asisopropyl chloride with Lewis acid catalyst, and interhalogen compoundssuch as IBr and ICl. Furthermore, heavier FHD-103X halides can beconverted to lighter halides utilizing the appropriate lighter silverhalide (e.g. FHD-103Br and AgCl will produce FHD-103Cl). The phenolicalcohols of FHD-103X (X═F, Cl, Br, I) can be protected utilizingtert-butyl(chloro)diphenysilane and imidazole in DMF at RT to yieldFHD-104X (X═F, Cl, Br, I).

FIG. 43 depicts a synthetic pathway for intermediate NHD-103X, fromwhich some of the other syntheses begin. The synthesis steps are asfollows: RHD-101 is subjected to strongly acidic conditions such asmethanesulfonic acid in the presence of 2,4,6-trifluoroaniline at roomtemperature to yield NHD-102. The use of Brønsted acidic conditionsfavors carbocation formation at the 3,5,7 bridgehead positions of theadamantane cage structure over redistribution reactivity at thegermanium center. To form NHD-103, NHD-102 is alkylated at roomtemperature with 4-methoxybenzyl bromide in DMF with potassium carbonatebase in the presence of potassium iodide. To form NHD-103X, the 1-methylgroup of NHD-103 can be exchanged with a halide (X═F, Cl, Br, I) with avariety of electrophilic reagents at low temperatures ranging from −78 Cup to room temperature depending on the halide desired. Reagentsinclude, but are not limited to: Lewis acids such as SnCl4 or GaCl3,elemental halides Br2 and I2 with Lewis acid catalyst, alkyl halidessuch as isopropyl chloride with Lewis acid catalyst, and interhalogencompounds such as IBr and ICl. Furthermore, heavier NHD-103X halides canbe converted to lighter halides utilizing the appropriate lighter silverhalide (e.g. NHD-103Br and AgCl will produce NHD-103Cl).

Surface Preparation

Various exemplary surfaces are described herein, including diamond,silicon and gold. Preferably, these surfaces would more specifically bedepassivated diamond, partially-hydrogenated partially-chlorinatedSi(111), and Au(111). Of course, similar surfaces could be used,including germanium, and lead, although they may require leg or linkermodifications.

With respect to diamond, methods for obtaining surfaces appropriate forboth presentation of tips and building of workpieces are well known inthe literature (for example, see (Hayashi, Yamanaka et al., “Atomicforce microscopy study of atomically flat (001) diamond surfaces treatedwith hydrogen plasma,” Applied Surface Science. 1998. 125:120-124;Watanabe, Takeuchi et al., “Homoepitaxial diamond film with anatomically flat surface over a large area,” Diamond and RelatedMaterials. 1999. 8:1272-1276; Okushi, “High quality homoepitaxial CVDdiamond for electronic devices,” Diamond and Related Materials. 2001.10:281-288; Tokuda, Umezawa et al., “Atomically flat diamond (111)surface formation by homoepitaxial lateral growth,” Diamond and RelatedMaterials. 2008. 17:1051-1054; Yatsui, Nomura et al., “Realization of anatomically flat surface of diamond using dressed photon-phonon etching,”Journal of Physics D: Applied Physics. 2012. 45:475302)).

Partially-hydrogenated partially-chlorinated Si(111) is used inpreference to a fully-chlorinated Si surface because the partialchlorination reduces the energy barrier to the tip molecules binding ascompared to just chlorinated Si(111) because the hydrogen, being smallerin size than Cl, helps reduce steric congestion as the tip approachesthe surface. Hydrogenation is preferably in the 33%-50% range, althoughwider ranges will work, as will not using hydrogenation at all.Partially hydrogenated partially-chlorinated Si(111) can be prepared ina number of ways. One is the following.

Clean, atomically flat doped Si(111) surfaces are prepared by directcurrent annealing the Si for several hours at ˜650 C followed by rapidheating to ˜1200 C for 1-20 sec while keeping the chamberpressure<1×10-9 Torr. This procedure gives the 7×7 reconstructed Si(111)surface, as in J Phys Cond Matt 26, 394001 (2014).

The Si(111) surface can be chlorinated by depositing Cl2 from anelectrochemical cell similar to the one in J Vac Sci and Tech A 1, 1554(1983), while the Si(111) is heated to ˜400 C. Atomically flathalogenated Si(111) surfaces have been prepared this way, as in Phys RevLett 78, 98 (1997).

Si(111)-Cl surfaces can then be partially hydrogenated by exposing thesurface to 600 L of atomic hydrogen from a H2 cracker, as in Surf Sci402-404, 170-173 (1998), with the Si(111)-Cl at room temperature.

Clean, atomically flat Au(111) surfaces are prepared by repeated cyclesof sputtering and annealing a single crystal Au(111) surface, as in PhysRev Lett 80, 1469 (1998).

Tip Bonding

Once synthesized, a tip can be bound to a presentation surface,including large surfaces, and smaller surfaces such as meta-tips or asingle-tip tool surface. Many ways of binding tips to surfaces arepossible, and these may vary with the exact nature of the tip and thesurface.

One method of depositing isolated tips on a surface is via thermalevaporation in vacuum. In this technique, purified molecules in the formof a solid or liquid are heated up in a vacuum chamber until theyevaporate as a gas of isolated molecules. By placing the presentationsurface within this gas, individual tips will adhere to the surface.(See tetramantane deposition as described in “Spatially resolvedelectronic and vibronic properties of single diamondoid molecules,”Nature Materials 7, 38-42 (2008)). This method has the advantage ofdepositing molecules without surface contamination from a solvent andcan be used with masks. The use of masks allows creating sectors whichcould each contain different tips, or different mixtures of tips,allowing for logical and efficient layout of tips.

The tips having sulfur or thiol-based linkers will bond to goldspontaneously at room temperature. The tips with O or NH linkersdesigned to bond to chlorinated silicon surfaces require heating of thesurface to overcome reaction barriers. This is the reason partialhydrogenation/chlorination is favored: The reduction in stericinterference keeps the reaction barrier to tip binding as far below thetip decomposition temperature as possible.

A simple way to evaporate molecules is to place the molecules in a glassor alumina crucible with a tungsten wire wrapped around the crucible.Passing a current through the wire heats the crucible and molecules,generating a molecular gas that exits the front of the crucible. Athermocouple on the crucible measures its temperature. A quartz crystalmicrobalance can be used to determine how much is evaporating as afunction of time and temperature.

This is just one example of how tips could be bonded to a surface. Suchtechniques, including how to create sectors of specific molecules, arewell-known in the respective arts. (Zahl, Bammerlin et al., “All-in-onestatic and dynamic nanostencil atomic force microscopy/scanningtunneling microscopy system,” Review of Scientific Instruments. 2005.76:023707; Sidler, Cvetkovic et al., “Organic thin film transistors onflexible polyimide substrates fabricated by full-wafer stencillithography,” Sensors and Actuators A: Physical. 2010. 162:155-159;Vazquez-Mena, Gross et al., “Resistless nanofabrication by stencillithography: A review,” Microelectronic Engineering. 2015. 132:236-254;Yesilkoy, Flauraud et al., “3D nanostructures fabricated by advancedstencil lithography,” Nanoscale. 2016. 8:4945-50)

Tip Activation

Tips, particularly those with exposed radicals at their active site, maybe bonded to a surface in an inactive form. One method of activatingsuch tips is through photo-cleavage of the structure. For example, thehalogen-capped tip examples herein can be activated through exposure to254 nm light. FIG. 44 depicts an activating reaction for halogen-cappedtips. Other wavelengths and chemistries can also be used. For example,if different synthetic steps were used, a tip could be protected with aBarton ester, which can then be cleaved, activating the tip, with 365 nmlight. FIG. 45 provides an example of the activation reaction that couldbe used with a Barton ester.

While not the only way to remove a tip cap, photo-activation isconvenient in that different areas of a surface can be masked. Differentwavelengths can also be used, choosing wavelengths which affect sometips but not others. This makes photo-activation a versatile techniqueeven when multiple types of tips are present, or whenpotentially-complex layout patterns are desired.

Barton Ester Caps

Other examples are provided herein of synthetic routes to halogen-cappedtips, and how to activate them. To demonstrate another chemistry forsynthesizing tips with protective caps, the Barton ester is analternative that fragments upon being irradiated with, for example,355-365 nm wavelength light to give the carbon centered radical, CO2,and the pyrithiyl radical. (Barton, D. H. R., Crich, D., Potier, P.Tetrahedron Lett., 1985, 26, 5943-5946. For a review of thiohydroxamicacids chemistry see: Crich, D., Quintero, L. Chem. Rev. 1989, 89,1413-1432) These types of activated molecules can be made from thedescribed compounds and one such synthetic route is described below,resulting in the Barton ester version of the AbstractionO tip.

FIG. 46 depicts the synthesis of the Barton ester AbstractionO tip,which is as follows: To synthesize the Barton ester for photoactivation,propynoic acid OFAB-1 is made from OFA-7 using the traditionalCorey-Fuchs procedure and quenching by bubbling gaseous CO2 through thereaction mixture. (Corey, E. J., Fuchs, P. L. Tetrahedron Lett. 1972,36, 3769-3772) The first step forms the 1,1-dibromoalkene in solution at−78 C. The addition of 2 more equivalents of butyllithium forms thelithium acetylide in the reaction mixture. By bubbling with the carbondioxide the desired carboxylic acid OFAB-1 is obtained after an aqueousworkup. To make the Barton ester, carboxylic acid derivative OFAB-1 isactivated to the acid halide by oxalic acid and catalyticN,N-dimethylformamide (DMF) in dichloromethane at room temperature. Tothis reaction mixture the sodium pyrithione salt is added to the mixtureto form the desired ester bond in compound OFAB-2. The Barton ester isunstable to aqueous acidic and basic media, so careful control ofreaction conditions must be taken when removing the protective groups.Multiple techniques are possible for removal of silyl ethers such asOFAB-2 that are pH sensitive. One is to use more labile silyl etherssuch as trimethylsilyl- (TMS-) or triethylsilyl- (TES-) ethers in placeof the more stable TBS silyl ethers. Another method is to use OFAB-2 andcatalytic solid tetra-n-butylammonium fluoride (TBAF) or cesium fluoridein 100:1 THF-buffer solution to produce OFAB-3. A solution of K2HPO4buffered at pH=7.1 could be used in the TBAF deprotection. (DiLauro, A.M.; Seo, W.; Phillips, S. T., J. Org. Chem. 2011, 76, 7352-7358) Thisdecreases the risk of hydrolyzing the Barton ester bond and increasesthe likelihood of obtaining the free phenols in OFAB-3, the Barton esterAbstractionO tip.

Methods of Tip Use

One of the ways in which surface mounted tips can be used is depicted inFIG. 47. This figure is diagrammatic and not to scale. In FIG. 47,handle 4701 is connected to surface 4702. Surface 4702 is optional,serving to provide the desired materials and chemistry to bind workpiece4703 in the case where the material of the handle is unsuitable fordoing this directly. It may be possible to bind workpiece 4703 directlyto handle 4701. Handle 4701 would be connected to a positional means(not shown) for the purposes of moving handle 4701, and therebyworkpiece 4703 with respect to tips (of which tip 4704 isrepresentative) mounted on surface 4705.

In the depicted position, workpiece 4703 could be descending upon a tip,or it could be rising from just having been acted upon by a tip.Regardless, the point is that surface 4705 can contain many tips, ofmany different types, including non-functional tips (which either failedto synthesize correctly or have already been used). Knowledge of tipposition, for example, because sectoring was used to place certain tiptypes in certain locations, or via scanning the surface (before orduring a build sequence), allows the workpiece to be moved to a desiredtip, at which time a mechanosynthetic reaction occurs, and the workpiecethen moves to the next desired tip. This process is repeated until theworkpiece is complete.

Another way to use surface-mounted tips is to create a meta-tip, whichis a handle upon which a plurality of tips may be mounted, directly, orvia a surface. FIG. 48 depicts this mode of using surface-mounted tips,where handle 4801 is connected to (optional) surface 4802. Handle 4801is also connected to a positional means (not shown). Tips, of which tip4804 is representative, are shown mounted on surface 4802, but could bemounted directly to handle 4801. In this scenario, the tips move to actupon workpiece 4803, which resides upon surface 4805.

The main difference between the scenarios of FIG. 47 and FIG. 48 iswhether the workpiece moves or the tips move. In actuality, it ispossible that both move (e.g., one for course adjustments, one forfine), and the distinction is mainly one of equipment design.

FIG. 48 perhaps provides the clearest illustration of the advantagessurface-mounted tips have over previous mechanosynthesis techniques. Ifsurface 4802 only had one tip affixed to it, it would be analogous tothe tips commonly used for mechanosynthesis. In this scenario, to createcomplex workpieces, the affixed tip would have to a) be capable ofmultiple reactions and b) be regenerated frequently, or, frequent tipswapping employed. Using either the scenario of FIG. 47 or FIG. 48 (andmodifications thereof which would be possible given the teachingsherein), many tips are available to provide mechanosynthetic reactions,potentially (depending on the number of tips initially available and thenumber of reactions required to build the workpiece) without tiprecharge and without tip swapping. Any reduction in tip recharge or tipswapping can help decrease the average time it takes to perform areaction.

Number of Available Tips

The total number of available tips could span a very wide range,depending on factors such as the total number of reactions needed tomake a workpiece, the number of different types of reactions needed tomake a workpiece, the available size of the presentation surface, andthe exact methods being used. Also, it is conceptually important todistinguish between the total number of available tips, and the numberof different types of tips.

For example, if tip recharge is acceptable, then the number of tipsmight be limited to only providing one tip for each type of reactionneeded by a build sequence. For example, as described herein, one way ofbuilding diamond requires four different tips (and row initiation andtermination each take only three tips, while row extension requiresfour). Ignoring feedstock and differences only in legs or linkers, about7 different types of tips are described herein. Counting feedstock,given the structures in Table 1, in addition to those in, e.g., FIGS.1-17 and FIG. 51, this number becomes about 20 or more since some tipscan use a variety of feedstocks. Given these examples, it will beobvious that the number of types of tips present in a system can includeless than 4, 4 to 7, 8 to 20, or more. Note that this says nothing aboutthe number of positional means in a system, since multiple types of tipscan be affixed to a single positional means.

Having a single tip of any required type present is useful for avoidingtip swapping, but not as useful for avoiding tip recharge. To avoid tiprecharge, ideally each type of tip would be present at least as manytimes as that tip is used in a build sequence. Given that buildsequences can essentially be arbitrarily long, this is one example whereit becomes useful to have the total number of tips present be, e.g., 10to 100 for even quite small workpieces, and between one hundred and athousand, or between a thousand and a million, or between a million anda billion, or more, for larger workpieces. It can easily be seen bydetermining the surface area available to an appropriate system, and thesize of the average tip, that even while allowing for some wasted spacegiven, for example, imperfect tiling of tips on a presentation surfaceand the possible presence of some percentage of defective tips, thepresentation surface can hold a very large number of tips.

Mechanosynthesis-Adapted Equipment

Typical commercial atomic microscopy systems combine course and finemotion controllers to provide both long range of motion, and atomicresolution. Multi-tip systems are also available (or can be constructed,for example (Eder, Kotakoski et al., “Probing from both sides: reshapingthe graphene landscape via face-to-face dual-probe microscopy,” NanoLetters. 2013. 13:1934-40)), whereby more than one tip can be employedsimultaneously. For example, Omicron's (Scienta Omicron GmbH, Germany)LT Nanoprobe provides a pre-integrated SPM, having 4 probe tips, acourse motion controller with a range of 5 mm×5 mm×3 mm, a fine motioncontroller with a range of 1 um×1 um×0.3 um, and atomic resolution inSTM mode. Such equipment suffices for mechanosynthesis work, and giventhat mechanosynthesis work has been carried out for decades, even whatwould currently be considered outdated equipment can suffice. However,typical SPM equipment is not optimized for carrying out high-volumemechanosynthetic reactions. Typical SPM work involves analysis ratherthan manufacture, the point generally being to scan specimens to createan image or collect other data. Scan speed is frequently the limitingfactor, and increasing scan speed is an active area of research (Dai,Zhu et al., “High-speed metrological large range AFM,” MeasurementScience and Technology. 2015. 26:095402).

Scan speed is less important to systems for mechanosynthesis as long asthe system can obtain the necessary accuracy without scanning, which iswell within the state-of-the-art. Ideally, systems adapted formechanosynthesis would not need to scan, at least for positiondetermination or refinement. Realistically, some scanning will probablybe necessary, including an initial surface scan to map surface topologyand tip location and identity, and, if desired, small areas around areaction site could be scanned after a reaction to verify that thereaction occurred correctly (it should be noted that this may not benecessary given the extremely high reliability of many of the exemplaryreactions). Note that such scanning and tip or workpiececharacterization capabilities are clearly present in thestate-of-the-art; see for example (Giessibl, “Forces and frequencyshifts in atomic-resolution dynamic-force microscopy,” Physical ReviewB. American Physical Society. 1997. 56:16010-16015; Perez, Stich et al.,“Surface-tip interactions in noncontact atomic-force microscopy onreactive surfaces: Si(111),” PHYSICAL REVIEW B. 1998. 58:10835-10849;Pou, Ghasemi et al., “Structure and stability of semiconductor tipapexes for atomic force microscopy,” Nanotechnology. 2009. 20:264015;Yurtsever, Sugimoto et al., “Force mapping on a partially H-coveredSi(111)-(7×7) surface: Influence of tip and surface reactivity,”Physical Review B. 2013. 87; Hofmann, Pielmeier et al., “Chemical andcrystallographic characterization of the tip apex in scanning probemicroscopy,” Phys Rev Lett. 2014. 112:066101; Hapala, Ondráček et al.,“Simultaneous nc-AFM/STM Measurements with Atomic Resolution,”Noncontact Atomic Force Microscopy: Volume 3. Cham, SpringerInternational Publishing. 2015.29-49).

Regardless of the fact that some scanning will likely be used at variouspoints in the mechanosynthetic process, doing away with frequentscanning for position refinement, and instead using metrology thatallows the requisite point-to-point accuracy (meaning, moving directlyfrom one tip or workpiece location to another, without using scanning inbetween to refine position), would considerably speed up the process ofmechanosynthesis.

Note that while the ideal attributes for analytical or metrological SPMare different than those for systems for mechanosynthesis, even previouswork on mechanosynthesis did not provide systems well-adapted for suchwork, presumably due to the simple and low-volume nature of the workbeing performed, for which conventional equipment suffices. For example,many commercial atomic microscopes are open-loop, meaning, they do notuse metrology to refine tip position. However, closed-loop systems arealso available, can be built, or metrology can be added to an existingopen-loop system (e.g., see (Silver, Zou et al., “Atomic-resolutionmeasurements with a new tunable diode laser-based interferometer,”Optical Engineering. 2004. 43:79-86)). Closed-loop systems are generallymore accurate due to metrology feedback and positional means capable ofvery high accuracy over large distances are available. For example,piezo elements are often used to position tips very precisely, and usinginterferometry, angstrom or even picometer-level accuracy has been shownto be possible, even at distances up to 50 mm. (Lawall, “Fabry-Perotmetrology for displacements up to 50 mm,” J. Opt. Soc. Am. A. OSA. 2005.22:2786-2798; Durand, Lawall et al., “Fabry-Perot DisplacementInterferometry for Next-Generation Calculable Capacitor,”Instrumentation and Measurement, IEEE Transactions on. 2011.60:2673-2677; Durand, Lawall et al., “High-accuracy Fabry-Perotdisplacement interferometry using fiber lasers,” Meas. Sci. Technol.2011. 22:1-6; Chen, Xu et al., “Laser straightness interferometer systemwith rotational error compensation and simultaneous measurement of sixdegrees of freedom error parameters,” Optics Express. 2015. 23:22)Further, although this could be unnecessary with high-accuracy closedloop systems, software capable of compensating for positional errors dueto hysteresis, creep, and other phenomenon is available; for example see(Mokaberi and Requicha, “Compensation of Scanner Creep and Hysteresisfor AFM Nanomanipulation,” IEEE Transactions on Automation Science andEngineering. 2008. 5:197-206; Randall, Lyding et al., “Atomic precisionlithography on Si,” Journal of Vacuum Science & Technology B:Microelectronics and Nanometer Structures. 2009. 27:2764; Follin, Tayloret al., “Three-axis correction of distortion due to positional drift inscanning probe microscopy,” Rev Sci Instrum. 2012. 83:083711). Softwarealso exists that essentially uses image recognition for positionalrefinement; for example see (Lapshin, “Feature-oriented scanningmethodology for probe microscopy and nanotechnology,” Nanotechnology.2004. 15:1135-1151; Lapshin, “Automatic drift elimination in probemicroscope images based on techniques of counter-scanning and topographyfeature recognition,” Measurement Science and Technology. 2007.18:907-927; Lapshin, “Feature-Oriented Scanning Probe Microscopy,”Encyclopedia of Nanoscience and Nanotechnology. 2011. 14:105-115).Ideally, this would not be necessary since the required scanning wouldslow down the overall process, but it is available if desired.

Note that 50 mm is far longer than the working distance needed toaccommodate a very large number of tips (billions, trillions, or more)and complex workpieces. Distances on the order of microns (or evensmaller for small workpieces), thousands of times smaller than thetechnology has been proven capable of, would suffice for many types ofworkpieces.

In a metrological system, the tip is generally not exactly at the pointbeing measured (which may be, e.g., a reflective flat when using laserinterferometry), such metrology has to be carefully implemented toavoid, e.g., Abbe error which can be induced by slightly non-linearmovement of the tip or workpiece with respect to, e.g., the reflectiveflat. One way to address this issue it to measure not only the X, Y andZ coordinates of the reflective flat, but also to measure (and so beable to account for) any rotation that might be occurring around theseaxis as well.

One way to measure both linear and angular position is to use 6interferometers (e.g., Michelson or Fabry-Perot opticalinterferometers). FIG. 49 illustrates one way interferometers can beused to measure six degrees of freedom (X, Y, and Z, and rotation abouteach of those axes).

In FIG. 49, Reflective mirrors 4901-4906 and, and their respectivebeams, BeamZ1 4907, BeamZ2 4908, BeamZ3 4909, BeamX1 4910, BeamY1 4911and Beam Y2 4912 can be used together to determine position in all sixdegrees or freedom. The spacing between various pairs of beams must beknown to compute rotations. In this scenario, BeamX1 provides the Xposition. BeamY1 or BeamY2 provide the Y position. BeamZ1, or BeamZ2, orBeamZ3 provides the Z position. BeamZ1 and BeamZ2, together with thedistance between the two beams allows the rotation about the X axis tobe calculated. BeamZ2 and BeamZ3, together with the distance between thetwo beams allows the rotation about the Y axis to be calculated. And,BeamY1 and BeamY2, together with the distance between the two beamsallows the rotation about the Z axis to be calculated.

Coupling the ability to provide, ideally, sub-Angstrom linear distancemeasurement over distances up to the millimeter scale, while alsomeasuring and accounting for angular errors, with, for example, amicroscope that operates at 4K (room temperature is feasible but moretechnically challenging) in ultra-high vacuum, while using, e.g., aqPlus sensor, provides for a system that can access precise locations onlarge presentation surfaces with a greatly-reduced need to use scanningand image recognition to refine the relative position of tips andworkpieces. These adaptations themselves are valuable formechanosynthesis. Using such equipment with surface-mounted tips and theprocesses described herein provides systems adapted for mechanosynthesisthat can provide much greater reaction throughput than conventionalsystems.

Other useful adaptations that are somewhat unique to the requirements ofmechanosynthesis include reducing tip recharge and reducing tip swapping(which does occur in more conventional uses of SPM equipment, butnormally because a tip has been damaged, not because many tips ofdifferent chemical natures are required). Surface mounted tips have beendiscussed herein as one way to reduce the need for tip recharge and tipswapping.

Sequential Tip Method

Surface-mounted tips and inverted mode offer important improvements overconventional mode. However, inverted mode, because the workpiece isbeing built on the handle (e.g., an SPM probe), does have somedrawbacks. For example, if the workpiece is not conductive, some modessuch as STM may not be possible. Also, the geometry of the workpiece canpose a problem. For example, if a workpiece has a sizeable flat surfaceadjacent to the site of the next reaction, as the reaction site on theworkpiece approaches the surface-mounted tips, other portions of theworkpiece will also be approaching other surface-mounted tips,potentially causing undesired reactions. Ideally, one would like tocombine the benefits of both inverted mode and conventional mode,keeping the high aspect ratio, versatile mode capabilities and otherdesirable characteristics of conventional mode, without sacrificing theimportant improvements that inverted mode with surface mounted tipsoffers, such as the reduction or elimination of tip swapping due to theavailability of large numbers of any type of tips required for a givenbuild sequence, and the elimination of feedstock provisioning and trashdepots as separate entities from surface-mounted tips.

Obtaining the benefits of both inverted mode with surface-mounted tipsand conventional mode is possible if the tip thermodynamics areengineered to allow an additional tip-to-tip feedstock transfer,resulting in what we refer to as a “thermodynamic cascade.” Rather thana surface-mounted tip interacting directly with the workpiece, thesequential tip method consists of a surface-mounted tip interacting witha conventional mode tip. The conventional mode tip interacts with theworkpiece. The surface mounted tips thus serve as what can beconceptualized as a surface with tunable affinity. Since the surfacemounted tips can be engineered to have any desired affinity for theirfeedstock, they can present or accept a much wider range of feedstocksto the conventional tip than would be possible if the feedstock wasattached directly to the presentation surface. Note that the workpieceis preferably located on the presentation surface along with the surfacemounted tips, although this is not always true, as is explained herein.

FIG. 50a-f shows one way of implementing the sequential tip method, withsub-FIGS. 50a-e depicting sequential states of the same system and FIG.50f showing an overhead view.

FIG. 50a , which we arbitrarily use as a starting state, shows handle5001 (which would be connected to positional control means, not shown)with a tip 5003 (a conventional mode tip) bound to its apex. Tip 5003has an active site 5002, which in this case, is empty and awaitingfeedstock. A presentation surface 5007 holds tips, of which tip 5004 (aninverted mode tip) is exemplary, and a workpiece 5006. The tip 5004includes feedstock 5005.

In FIG. 50b , handle 5001 and tip 5003 have been positioned so thatactive site 5002 binds to feedstock 5005. In other words, amechanosynthetic reaction occurs between tip 5003 and feedstock 5005. Atthis point, feedstock 5005 is bound to both tip 5003 and tip 5004.

In FIG. 50c , handle 5001, and thus tip 5003, have been pulled away fromtip 5004, and feedstock 5005 has transferred to tip 5003. This transferoccurs upon pulling the two tips away from each other because tip 5003has been engineered to have greater affinity for feedstock 5005 than tip5004.

In FIG. 50d , handle 5001 brings tip 5003 and its feedstock 5005 to aspecific location on workpiece 5006, facilitating a mechanosyntheticreaction between feedstock 5005 and workpiece 5006. At this pointfeedstock 5005 is bound to both tip 5003 and workpiece 5006.

In FIG. 50e , handle 5001 and tip 5003 have been pulled away fromworkpiece 5006, leaving feedstock 5005 bound to workpiece 5006. Like theprevious tip-to-tip transfer between tip 5004 and tip 5003, feedstock5005 remains bound to workpiece 5006, instead of pulling away with tip5003, because tip 5003 has been engineered to have lower affinity forfeedstock 5005 than does the chosen specific location on workpiece 5006.

FIG. 50f depicts a top view of the system shown in side views in FIG.50a-e . Workpiece 5006 is shown partially under handle 5001 (dottedlines representing the hidden borders of the workpiece) and tip 5003(denoted with dotted lines as it is under handle 5001). Tip 5004 isrepresentative of many surface-mounted tips arrayed in sectors set offby a grid of dotted lines, such as exemplary sector 5008. Of course,this is not to scale, nor necessarily the actual arrangement that wouldbe used. The workpiece could be next to the surface-mounted tips, in themiddle of the surface-mounted tips, or at any other convenient location,even on a different presentation surface. The sectors could berectangular, concentric, shaped like pie wedges, or any other convenientshape, or sectors could not exist at all, with tips of different typesbeing intermingled.

The addition of the tip-to-tip transfer step may complicate the systemdesign from a chemical perspective, but overall creates a more efficientand versatile system. The increased chemical complexity stems from thefact that to carry out the sequential tip method, assuming a donationreaction, the affinity of the surface-mounted tip for the feedstock mustbe less than the affinity of the conventional tip for the feedstock (arequirement that does not exist in conventional or inverted mode, sinceno tip-to-tip transfer takes place), and the affinity of theconventional tip for the feedstock must be less than the affinity of theworkpiece for the feedstock.

The chemistry is further complicated by the desire to have a singleconventional tip be able to receive many different feedstocks fromsurface-mounted tips, and be able to donate those feedstocks to variousspecific locations on a workpiece, which may vary in their chemicalnature, and therefore in their affinity for feedstock. Note that whilethese reactions are generally described in terms of a tip donatingfeedstock to a workpiece, the same principles apply to abstractionreactions, although the thermodynamics and sequence of events need to bechanged as appropriate.

Subsequently, we describe how to design and build tips, both surfacemounted and conventional, that meet the necessary thermodynamicrequirements. We also provide a work-around for situations where it isnot possible or desirable for one conventional tip to carry out all thereactions of a given build sequence.

Note that, while the sequential tip method is generally described asinvolving two tips and therefore a single tip-to-tip transfer for agiven reaction on a workpiece, if desired, there is no reason thesequential tip method could not be performed with more than two tips aslong as the tip affinities are appropriately designed.

Tip Design for the Sequential Tip Method

Two types of tips are used in the sequential tip method: surface-mountedtips and conventional tips. Herein we describe a set of tips that can beused as surface-mounted tips and allow the transfer of a wide variety offeedstock (including atoms abstracted from a workpiece, such as with theAbstractionO, AbstractionNH and AbstractionS tips). Using thesesurface-mounted tips as examples, we now turn to the design of aconventional tip which has an affinity for many of the variousfeedstocks which is between that of the surface-mounted tips and that ofan exemplary diamond workpiece.

Note that in mechanosynthetic reactions it is not necessarily the energylevels of the products and reactants that specify their relativeaffinities. Bond stiffness is also a factor. Consider the hypotheticalreaction Tip-F+Workpiece→Tip-+F-Workpiece. It is possible that thereactants have lower energy than the products. However, themechanosynthetic reaction can still be successful if the F-Workpiecebond is stiffer than the Tip-F bond. In such a case, as the tip isretracted from the workpiece, the Tip-F bond gradually stretches andthen breaks, unable to overcome the stiffness of the F-Workpiece bond,even though the overall energy of the Tip-F bond may be greater. This isnot merely hypothetical; some of the reactions of which the exemplarytips are capable work in this manner. Given this, affinity is notdefined by bond energy. Rather, we use the practical definition thatwhen two structures (e.g., two tips, or a tip and a surface, or a tipand a workpiece, or a workpiece and a surface) are brought together topotentially transfer feedstock in a mechanosynthetic reaction, thestructure to which the feedstock is bound after the two structures areseparated has the higher affinity for that feedstock.

FIG. 51 depicts one possible structure of a conventional tip for use inthe sequential tip method. The tip is built on surface 5101 (which wouldbe connected to a positional means, not shown) and comprises supportatoms 5102, 5103 and 5104, and active atom 5105. In this state, activeatom 5105 is a radical, ready to e.g., bind feedstock fromsurface-mounted tips, or abstract one or more atoms from a workpiece.Passivating atom 5106 is used to satisfy unused valences, and isrepresentative of many such atoms bonded to the tip and surface.

In one embodiment, surface 5101 is silicon, support atoms 5102, 5103 and5104 are carbon, and active atom 5105 is silicon. For buildingdiamond-based structures, this embodiment has an affinity which isconveniently between that of the described surface-mounted tips and theworkpiece for multiple different feedstocks and reactions. In oneembodiment passivating atom 5106 and other passivating atoms could beany atom of appropriate chemical nature such as hydrogen or fluorine.

We refer to the embodiment where the active atom is silicon, connectedto three support atoms which are carbon, as half-Si-Rad (because it is apartial or “half” adamantane structure with an apical silicon radical inits basic form). With various feedstock attached, the tip can take formswhich include half-Si-Rad-CC (a carbon dimer bound to the active atom,and a radical itself, which for some reactions actually makes the apicalcarbon of the carbon dimer the active atom as it can be used to abstractother atoms from tips or workpieces), half-Si-Rad-H (a hydrogen bound tothe active atom), and half-Si-Rad-CH2 (CH2 bound to the active atom),among others.

Exemplary reactions that various versions of the half-Si-Rad tip cancarry out include: H Abstraction from C(111) to half-Si-Rad-CC, HDonation to from half-Si-Rad-H to C(111)-Radical, H Abstraction fromC(111)-CH3 to half-Si-Rad-CC, H Donation from half-Si-Rad-H toC(111)-CH2, CH2 Donation from half-Si-Rad-CH2 to C(111)-Radical, CH2Donation from half-Si-Rad to C(111)-CH2 and C2 Dimer Donation fromhalf-Si-Rad-CC to C(111)-Radical.

While half-Si-Rad can carry out many useful reactions, it is not capableof carrying out all reactions, particularly when different classes ofworkpieces are considered. For example, silicon bonds tend to be weakerthan carbon bonds, and germanium bonds tend to be weaker still. Giventhis, for Si- or Ge-based workpieces, the half-Si-Rad tip will oftenhave an affinity for feedstock that is higher than the affinity of theworkpiece for the feedstock. This means that it could not donate thefeedstock to the workpiece. A systematic method of adjusting tipaffinity would be useful to assist in the rational design of tips withdifferent feedstock affinities. There are two main ways of adjusting tipaffinity without departing from the basic bonding structure of the tipdepicted in FIG. 51.

First, active atom 5105 can be substituted with an atom of differentaffinity. For example, to increase the affinity of the active atom forfeedstock, carbon could be substituted for silicon, and to reduce theaffinity of the active atom for feedstock, in order of descendingaffinity, germanium, tin, or lead could be used (although it should berecognized that this is a rule of thumb and will not be accurate for alltip-feedstock combinations; those familiar with the relevant arts willunderstand more nuanced ways of predicting affinity).

Second, one or more of the support atoms 5102, 5103 and 5104 can besubstituted with different atoms which can affect the affinity of activeatom 5105. For example, the embodiment described above where the supportatoms are each carbon is, for most diamond-based reactions, superior toan all-silicon tip because the affinity of the all-silicon tip is lowerthan desired. The carbon atoms strengthen the bond between the activeatom and the feedstock. Our computational studies indicate that activeatom affinity for feedstock, in general, is affected by the supportatoms in the following manner: O>N>C>S>P>Si. Meaning, using oxygen as asupport atom results in the highest affinity of the active atom for thefeedstock, while using silicon results in the lowest affinity of theactive atom for the feedstock, although like the affinity commentsabove, this is a rule of thumb. Regardless, this hierarchy provides auseful starting point for the design of new tips. Obviously, tips withdifferent basic structures, but with the desired feedstock affinity,could also be designed given the examples and teachings herein.

The ability to rationally design new conventional tips raises the issueof how these tips can be synthesized and bound to the positional means.While we could design and affix conventional tips in a manner like thatdescribed for surface-mounted tips, this would likely mean that multiplehandles, each with a different tip, would be needed. Assuming a singlepositional means, this implies that tip swapping would be required. Tipswapping is, as described herein, preferably avoided. Using equipmentwith multiple positional means is one way to overcome this problem. Forexample, systems with two to four positional means exist, and if eachpositional means was affixed to a tip of different affinity, the overallset of tips would allow a greater diversity of reactions than a singletip. However, multiple positional means complicates equipment design andincreases cost. A method to avoid tip swapping even with only a singlepositional means may be preferable.

In Situ Tip Synthesis

Tip swapping can be avoided if conventional tips are disassembled andreassembled (in modified form, as appropriate) on the same surface(e.g., a presentation surface connected to a handle) as needed. Forexample, if the half-Si-Rad tip described above was the initial tipbound to a handle, a build sequence could be carried out up until thepoint when a tip of different affinity was needed. At that point, theconventional tip (half-Si-Rad in this example) essentially becomes aworkpiece, with the system temporarily operating in inverted mode ratherthan sequential mode.

By this, it is meant that the surface-mounted tips act upon theconventional tip, modifying it as desired. The surface mounted tip canbe used to remove any (or all, creating a completely new structure) ofthe atoms in the conventional tip. The surface-mounted tips then providethe new atoms to manufacture a tip that can complete the next part ofthe build sequence. This process can be repeated as many times asnecessary to complete a build sequence, although preferably the need tochange the conventional tip would be minimized to streamline themanufacturing process. This suggests a refinement to the process ofcreating a build sequence where build sequences are ordered, at least inpart, in a manner that minimizes the need to rebuild the conventionaltips.

As an example of in situ tip synthesis, FIGS. 52a-o depict a buildsequence which creates the half-Si-Rad tip starting from a depassivatedsilicon surface. Depassivated silicon surfaces are well-known in therelevant fields, and can be created via bulk chemical methods orheating. Also, a patch of depassivated silicon atoms could be createdusing mechanosynthesis. For example, starting with a conventionalpassivated silicon probe, three hydrogens could be removed from a smallflat area on the apical end via the abstraction tips described herein.

In FIG. 52a , an exemplary silicon structure is depicted as astand-alone structure terminated with passivating hydrogens, of whichhydrogen atom 5201 is representative, except on its lower face, which isdepassivated. In reality, the structure depicted would be part of alarger structure (which may itself be connected to larger structuressuch as a handle and positioning means), but only the small area neededfor a presentation surface is shown for clarity. Three depassivatedsilicon atoms are present, of which silicon atom 5202 is representative.This silicon structure, with its small patch of depassivated siliconatoms, serves as the starting point for building the half-Si-rad tip.

In FIG. 52b , a bromine atom is donated to one of the depassivatedsilicon atoms. This can be accomplished with a tip comprising anadamantane body with a carbon radical active site, to which a bromineatom has been bound. We will refer to this tip as AdamRad-Br.

In FIG. 52c , another bromine atom has been added to one of the otherdepassivated silicon atoms, also using an AdamRad-Br.

In FIG. 52d , the third and final bromine is added to the lastunpassivated silicon atom, again using AdamRad-Br.

Note that the three bromine atoms which were added in the first threesteps of this sequence will end up being removed. This raises thequestion of why the bromine atoms were added in the first place. Thereason is that it is preferable to satisfy the valences of thedepassivated silicon atoms at certain points in the sequence to preventunwanted rearrangements (a useful technique in many build sequences).The question might also be raised as to why the sequence does not juststart from a hydrogenated silicon surface, since on that surface thereare no unused valences to lead to potential reactivity problems. Theissue is one of chemical convenience. Hydrogen, and in general,passivating atoms other than bromine, could be made to work. However,using the particular tips we have chosen for this sequence, bromine isfound to more reliably facilitate the desired reactions than other atomsthat were investigated.

In FIG. 52e , the structure shows that one of the bromine atoms has beenremoved. This is accomplished using a GeRad tip.

In FIG. 52f , a CH2 group has been added to the radical silicon that wascreated by the bromine removal in the previous step. This CH2 donationreaction is accomplished using a tip like MeDonationO or its variants,described herein.

In FIG. 52g , a hydrogen atom is added to the CH2 radical that was addedin the previous step. This is accomplished using HDonation (whether itis HDonationNH, HDonationO, or HDonationS not being relevant to thereaction).

In FIG. 52h , one of the remaining bromine atoms is removed, usingGeRad.

In FIG. 52i , a methyl group is donated to the silicon radical that wascreated by the bromine abstraction in the previous step. The methyldonation reaction is accomplished using MeDonation (again, the specificvariant not being relevant).

In FIG. 52j , the methyl group donated by the MeDonation tool in theprevious step is given a hydrogen atom, using an HDonation tip.

In FIG. 52k , the sole remaining bromine is removed from the structure,using GeRad.

In FIG. 52l , a methyl group is donated to the silicon radical that wascreated by the bromine abstraction in the previous step. The methyldonation reaction is accomplished using an MeDonation tip. Note thatunlike the previous methyl groups, this methyl group does not have itsopen valence satisfied via a hydrogen donation reaction.

In FIG. 52m , one of the previously-created CH3 groups has a hydrogenabstracted from it, via an Abstraction tip, resulting in a surface thathas two CH2 groups and one CH3 group.

In FIG. 52n , the remaining previously-created CH3 group has a hydrogenabstracted from it, via an Abstraction tip, resulting in three CH2groups on the surface of the structure.

In FIG. 52o , a silicon atom is bound to all three CH2 groups. Thesilicon atom is donated from an already-described tip loaded with adifferent payload. Specifically, the Abstraction tip can have a siliconatom bound to its radical active site, and will then donate that siliconatom to the structure. The Abstraction tip can be charged with a siliconfeedstock atom by abstracting a Si atom from anywhere else on theconventional tip which is not crucial to the build sequence. Theresulting structure is the half-Si-rad tip, which will be obvious whenrealizing that the structure shown in FIG. 52o , although differing inhow termination is depicted at the top of the diagram, is essentiallythe structure from FIG. 51.

The build sequence for the half-Si-Rad as described requires theAdamRad-Br tip. This is an adamantane radical with a bromine feedstock.The synthesis for this tip is depicted in FIG. 53. The synthesis startswith chemical SHA-2, previously described in FIG. 34 and the respectivesynthesis. SHA-2 can be iodinated at the 4-position of the aromaticrings using I2 and [bis(trifluoroacetoxy)iodo]benzene in CHCl3 to yieldAdBr-1. Sonogashira coupling conditions of AdBr-1 withtriisopropylsilylacetylene (TIPS acetylene) produces the protectedalkyne AdBr-2. Deprotection of the TIPS group proceeds with TBAF in THFto make the terminal acetylene AdBr-3. The terminal acetylene isdeprotonated with n-butyllithium at low temperature and paraformaldehydeis added to produce the tripropargylic alcohol AdBr-4, also calledAdamRad-Br. Note that this version of AdamRad-Br depicts a new legstructure, phenylpropargyl alcohol, which has been found to be useful inconjunction with adamantane-based bodies and silicon surfaces and couldbe coupled with any of the other tips described herein.

Note that it is possible to perform a modified version of thehalf-Si-Rad build sequence without using AdamRad-Br at all. The onlypurpose AdamRad-Br serves in the build sequence is to brominate adepassivated silicon surface. If the silicon surface is bulk passivatedwith bromine, rather than the more common hydrogen, the build sequencecan start from a structure equivalent to that of FIG. 52d , eliminatingall the bromine donation reactions. Techniques for bulk bromination (andhalogenation in general) of silicon are known in the literature, e.g.,see (He, Patitsas et al., “Covalent bonding of thiophenes to Si(111) bya halogenation/thienylation route,” Chemical Physics Letters. 1998.286:508-514; Eves and Lopinski, “Formation and reactivity of highquality halogen terminated Si (111) surfaces,” Surface Science. 2005.579:89-96).

While the example given describes building a conventional tip usingsurface-mounted tips, this need not be the only such process. Forexample, conventional tips could build surface-mounted tips, usingeither feedstock from other surface-mounted tips, or feedstockprovisioned directly off presentation surfaces. This could be useful if,for example, there were one or more surface-mounted tips that were onlyneeded in small quantity and so it is more efficient to build themmechanosynthetically rather than via bulk chemistry.

Additional Tip Design Guidelines and Examples

Herein we have described many different tips, and how a modular tipdesign can facilitate the creation of new tips. Some other comments ontip structure and design criteria may further facilitate new tip andreaction design.

First, the use of a rigid tip geometry can be helpful so that the bondsbetween the apical atom and the other tip atoms do not deformexcessively or break as a feedstock atom is transferred. However, wherethere is a small or non-existent reaction barrier, this requirement maybe relaxed. For various reasons (e.g., ease of synthesis, tip size, tipaspect ratio) a rigid tip may not be desired, and relaxing therequirement expands the possible design space. For example, if a givenfeedstock-workpiece reaction requires no physical force (meaning, thereaction will simply occur if the feedstock is brought into proximity ofthe desired site on the workpiece) to surmount a reaction barrier, theremay be no need for a design with three or more legs. One or two legs maywork fine.

The tip shape preferably allows the tip to approach a workpiece andperform the desired reaction without steric hindrance, leading to theobservation that higher aspect ratios can be advantageous (althoughsteric considerations can also be addressed through reaction order, forexample, by avoiding the need for high aspect ratios). Further, tipgeometry could also be exploited to hold feedstock at a particularangle. For example, equipment limitations may dictate that, e.g., an SPMprobe, must be kept perpendicular to the work surface. But, there may bereactions where a perpendicular alignment of the feedstock with theworkpiece is not a desirable trajectory. In that case, it is possible todesign a tip that holds the feedstock at e.g., 45 degrees (or any otherangle desired) to the rest of the tip or handle.

With regards to a rigid tip geometry, a tetrahedral structure withrespect to the apical atom can be useful as, with a feedstock atom boundto one leg of the tetrahedron, the other three bonds serve to stabilizethe apical atom when force is applied during a reaction. However, othergeometries are possible. For example, in addition to VSEPR AX4(tetrahedral, or other variations of AX4), AX5 and higher hybridizationscan also provide the necessary free electrons to bond a feedstock atomwhile having the ability to form at least three other bonds to create arigid tip structure. However, the primary concern is simply whether ornot a given tip will reliably perform the intended reaction, andcertainly working tips can deviate from these suggestions.

To facilitate the design of new tips and reactions by example, and toprovide a library of known tips and reactions (which may in themselvesconstitute a set of tips and reactions sufficient for some buildsequences, and the availability of a set of pre-vetted reactionscertainly speeds up the build sequence design process), below we providea table of various donating structures (e.g., tips), receivingstructures (e.g., workpieces, although in the examples the receivingstructures are also tip-sized to facilitate computational analysis) andreactions which can be facilitated between the two. These structures andreactions have been vetted using multiple computational chemistryalgorithms and approaches, including B3LYP/6-311G(d,p) using theGaussian09 software package with default DFT grid size and convergencecriteria. Other computational chemistry algorithms and basis sets canalso be employed, as can multi-scale methods such as ONIOM.

Computational means (hardware) were generally individual or clusteredIntel CPU-based, multi-core servers, having between 8 and 256 GB RAM,solid state hard drives, and network interconnects as appropriate. Thishardware is only exemplary. Other computational means can be used (ascould other software). For example, processors may be CPU-, GPU-,ASIC-based, or other. Memory means or data storage means, both volatileand non-volatile, could also take many forms including various flavorsof RAM, hard drives, or Flash, among others.

The data provided include net energy changes and reaction barriers, andthe feedstock transferred includes Al, B, Be, Br, C, Cl, F, Ge, H, Ir,Li, Mg, N, Na, O, P, S, and Si. While many examples are provided, theyare indeed only examples. These are certainly not the only structuresand reactions that would be possible given the teachings presentedherein.

With respect to the reactions in Table 1, the tip always approached theworkpiece coaxially. “Coaxial” means that the bond that is being broken(e.g., the tip-feedstock bond) and the bond being formed (e.g., thefeedstock-workpiece bond) lie on the same line. The coaxial trajectoryhas been found to be reliably facilitate most reactions we have studied.This fact, along with the extensive data provided, should enable thefacile design of a vast number of related reactions. Also, (Tarasov,Akberova et al., “Optimal Tooltip Trajectories in a Hydrogen AbstractionTool Recharge Reaction Sequence for Positionally Controlled DiamondMechanosynthesis,” J. Comput. Theor. Nanosci., 2, 2010) teaches aprocess that may be used to determine other trajectories, and weincorporate by reference this material.

In the table below, “Tip” is the donating structure, “FS” (feedstock) isthe atom being transferred, “Workpiece” is the structure to which thefeedstock is transferred, “Delta (eV)” indicates the change in energyfor the reaction, and “Barrier (eV)” indicates the reaction barrier.

“300K” is the probability of reaction failure at 300 Kelvin (roomtemperature), while “77K” is the probability at 77 Kelvin (liquidnitrogen temperature). Scientific notation is used due to the very smallnumbers. These calculations were performed using the formulas disclosedin Code Listing 1. 300K and 77K are representative temperatures only.Any temperature at which the reactions are reliable enough for a givenpurpose could be used, and another common temperature, 4K, iseasily-accessible with liquid helium and would show much higherreliability figures. Also, it is noteworthy that most of the reactionslisted would have over 99.99% reliability even at room temperature.

With respect to the structures, C9H14[Al,B,N,P] have the apical atom, towhich the feedstock atom is attached, at the sidewall position of anadamantane frame. C9H15[C,Si,Ge] have the apical atom, to which thefeedstock atom is attached, at the bridgehead position of an adamantaneframe. The notation for the workpieces are the same, except that theapical atoms are listed first. For example, the reaction where a C914Altip using a Be feedstock atom donates the feedstock atom to CC9H15 couldbe expressed as:

AdamantaneSidewall-Al-Be.+.C-AdamantaneBridgeHead→AdamantaneSidewall-Al.+.Be-C-AdamantaneBridgeHead

TABLE 1 Element Transfers with Energy Calculations and Reliabilities atVarious Temperatures Delta Barrier Tip FS Workpiece (eV) (eV) 77 K 300 KC9H14Al Al CC9H15 −0.64 0.02 1.15E−42 1.72E−11 C9H14Al B NC9H14 −3.400.00 1.18E−222 1.09E−57 C9H14Al Be CC9H15 −1.46 0.00 2.39E−96 2.87E−25C9H14Al Be NC9H14 −2.71 0.00 1.14E−177 3.84E−46 C9H14Al H BC9H14 −1.050.15 4.94E−69 2.94E−18 C9H14Al H CC9H15 −0.90 0.22 1.77E−59 8.32E−16C9H14Al H SiC9H15 −0.49 0.23 1.06E−32 6.21E−09 C9H14Al Li NC9H14 −0.760.00 1.30E−50 1.57E−13 C9H14Al Mg BC9H14 −0.22 0.00 2.48E−15 1.78E−04C9H14Al Mg NC9H14 −0.61 0.00 1.53E−40 6.04E−11 C9H14Al N BC9H14 −1.730.04 6.14E−114 8.75E−30 C9H14Al P BC9H14 −0.75 0.14 1.47E−49 2.93E−13C9H14Al P NC9H14 −0.42 0.00 4.85E−28 9.76E−08 C9H14Al P SiC9H15 −0.210.00 3.30E−14 3.47E−04 C9H14Al S BC9H14 −0.90 0.00 2.69E−59 9.27E−16C9H14B Al CC9H15 −0.13 0.00 3.72E−09 6.86E−03 C9H14B Be NC9H14 −1.260.00 4.21E−83 7.19E−22 C9H14B Li NC9H14 −0.78 0.00 5.61E−52 7.01E−14C9H14B Na NC9H14 −0.13 0.00 3.15E−09 6.58E−03 C9H14N Br AlC9H14 −2.480.00 7.75E−163 2.46E−42 C9H14N S AlC9H14 −0.65 0.02 1.95E−43 1.09E−11C9H14N S BC9H14 −1.55 0.00 5.25E−102 1.01E−26 C9H14N S SiC9H15 −0.410.11 2.18E−27 1.44E−07 C9H14P Al NC9H14 −1.67 0.07 6.91E−110 9.60E−29C9H14P Mg AlC9H14 −0.05 0.00 6.87E−04 1.54E−01 C9H14P Mg BC9H14 −0.270.02 1.71E−18 2.75E−05 C9H14P P BC9H14 −0.87 0.07 1.31E−57 2.51E−15C9H15C Br AlC9H14 −1.23 0.01 3.73E−81 2.27E−21 C9H15C Br BC9H14 −1.500.00 1.44E−98 7.71E−26 C9H15C Br GeC9H15 −0.60 0.06 5.25E−40 8.28E−11C9H15C Br SiC9H15 −1.01 0.04 1.27E−66 1.22E−17 C9H15C Cl AlC9H14 −1.220.17 9.07E−81 2.86E−21 C9H15C Cl BC9H14 −1.62 0.18 8.02E−107 5.87E−28C9H15C Cl GeC9H15 −0.52 0.32 1.27E−34 2.00E−09 C9H15C Cl SiC9H15 −1.020.21 1.29E−67 6.79E−18 C9H15C Li NC9H14 −1.06 0.00 6.19E−70 1.72E−18C9H15C Mg NC9H14 −0.61 0.00 8.90E−41 5.25E−11 C9H15C O BC9H14 −2.68 0.001.58E−175 1.36E−45 C9H15C S AlC9H14 −0.88 0.00 2.90E−58 1.71E−15 C9H15CS BC9H14 −1.78 0.00 7.93E−117 1.59E−30 C9H15C S GeC9H15 −0.24 0.002.11E−16 9.47E−05 C9H15C S NC9H14 −0.23 0.00 1.49E−15 1.56E−04 C9H15C SSiC9H15 −0.63 0.00 3.25E−42 2.25E−11 C9H15Ge Br AlC9H14 −0.63 0.117.10E−42 2.75E−11 C9H15Ge Br BC9H14 −0.90 0.14 2.73E−59 9.31E−16 C9H15GeBr SiC9H15 −0.41 0.21 2.39E−27 1.47E−07 C9H15Ge C CC9H15 −1.15 0.009.46E−76 5.54E−20 C9H15Ge C SiC9H15 −0.46 0.00 7.39E−31 1.85E−08 C9H15GeCl AlC9H14 −0.71 0.31 7.12E−47 1.43E−12 C9H15Ge Cl SiC9H15 −0.51 0.471.00E−33 3.39E−09 C9H15Ge F AlC9H14 −1.08 0.01 2.00E−71 7.15E−19 C9H15GeF BC9H14 −1.79 0.18 1.19E−117 9.76E−31 C9H15Ge Ge CC9H15 0.02 0.006.18E−02 4.89E−01 C9H15Ge H SiC9H15 −0.35 0.23 1.12E−23 1.29E−06 C9H15GeLi NC9H14 −0.46 0.00 1.62E−30 2.26E−08 C9H15Ge O BC9H14 −2.96 0.003.94E−194 2.29E−50 C9H15Ge O SiC9H15 −0.96 0.00 9.41E−64 6.66E−17C9H15Ge P BC9H14 −0.79 0.03 5.05E−52 6.82E−14 C9H15Ge S BC9H14 −1.540.15 3.71E−101 1.67E−26 C9H15Ge Si CC9H15 −0.21 0.00 3.21E−14 3.44E−04C9H15Si Al CC9H15 −0.25 0.02 4.97E−17 6.54E−05 C9H15Si B CC9H15 −1.120.14 4.39E−74 1.48E−19 C9H15Si Br BC9H14 −0.49 0.43 1.13E−32 6.31E−09C9H15Si H BC9H14 −0.56 0.27 4.65E−37 4.73E−10 C9H15Si Li NC9H14 −0.570.00 5.33E−38 2.71E−10 C9H15Si P BC9H14 −0.54 0.16 4.44E−36 8.44E−10C9H15Si S BC9H14 −1.14 0.00 2.44E−75 7.07E−20 C9H15Si Si CC9H15 −0.110.00 6.11E−08 1.41E−02 C9H15Si Ge CC9H15 −0.08 0.00 5.83E−06 4.53E−02C9H15Ge Ir CC9H15 −0.04 0.00 1.97E−03 2.02E−01 C9H15Ge Ir SiC9H15 −0.330.00 1.82E−22 2.63E−06 C9H15C Ir SiC9H15 −0.29 0.00 9.36E−20 1.31E−05C9H15C Ir BC9H14 −1.07 0.00 6.78E−71 9.77E−19

Note that it is possible for the change in energy (eV) to be positive.This is due to the fact that energy and force are not equivalent. Amechanosynthetic tip may exert force over a distance that results in anet change in energy which is positive, even if the reaction productresides in a local energy minima. This is discussed in more detailherein with respect to bond stiffness and affinity.

As the Table 1 data indicates, high reliability transfers of atomsincluding Al, B, Be, Br, C, Cl, F, Ge, H, Ir, Li, Mg, N, Na, O, P, S,and Si have been shown to be possible, using tips which employ activeatoms Al, B, C, Ge, N, P, and Si. Obviously, these are examples only,and an even wider range of tips and reactions can be designed given theteachings herein.

Bond Strain in Tip, Reaction and Workpiece Design

A number of strain types exist, such as Van der Waals, stretch, torsion,and angle (or “bend,” including ring) strain. In aggregate the varioustypes of strain are often referred to as “steric energies,” and thesesteric energies, or strain, are known to influence molecular stabilityand chemical reaction energetics.

For example, cyclobutane, with 7.5% kcal/mol/bond strain, is morereactive than the larger cycloalkanes in which the ring strain isrelaxed. Fullerenes are similarly affected by bond strain. Since thelowest energy configuration for individual fullerene units is planar,higher curvatures generally lead to more reactive molecules due at leastin part, to angle strain. In terms of individual bond energy, less thanabout 2% strain tends to have little effect on reactivity. 3-5% straintends to cause at least some increase in reactivity, while at 5-10%strain, major increases in reactivity are generally apparent. Of course,this trend cannot continue indefinitely; if strain is too high, a bondcan spontaneously rupture, leading to rearrangement of the molecule.

Note that overall, a molecule could have very little strain, but one ormore strained bonds can still cause it to be highly reactive, so thedistribution of strain is also important. Conversely, a molecule couldhave many bonds which are only slightly strained (perhaps less than the5% figure), yet when accumulated across multiple bonds, the overallstrain energy is substantial. In such cases, modest amounts of strain onper-bond basis can lead to substantial effects on molecule conformationand various other properties. These observations lead to the conclusionthat using strain to alter bond strength, and therefore reactivity, canbe a useful technique in the design of tips and workpieces.

One scenario is that of feedstock held to a tip by a single bond. Strainwithin the tip may be used to change the bond angles, and therebyenergies, of the apical tip atom to the feedstock. For example, consideran adamantane structure where a bridgehead carbon is bonded to thefeedstock. This bridgehead carbon would normally be bonded to threeother carbons, and the uniform length of the carbon-carbon bondsthroughout the adamantane structure allows the bridgehead carbon toachieve a perfect tetrahedral configuration where each bond to thebridgehead carbon is about 109.5 degrees. However, if a Ge atom issubstituted for each of the three carbons to which the bridgehead carbonis attached, the Ge—C-feedstock angle becomes about 112.9 degrees,causing angle strain.

In addition to angle strain, other type of strain can also be employed.For example, Van der Waals strain can be created by replacing, e.g., Hatoms with larger diameter atoms of the same valence, adjacent to thefeedstock. In this case, the larger diameter atom need not be bonded tothe feedstock or to the apical tip atom. It need only impinge upon thefeedstock's Van der Waals radius to cause steric strain.

While a tip designed in this manner can cause Van der Waals strain byhaving two or more parts of the same tip interfere (where one part isthe feedstock site and the other part is a portion of the tip designedto at least partially impinge upon the feedstock location), a second tipcould also be used to apply mechanical force to feedstock. For example,consider a first tip with feedstock bound to it. Using a second tip toapply force to the feedstock perpendicularly (or at any useful angle) toits point of attachment could weaken the bond between the first tip andthe feedstock. This is conceptually similar to building such strain intoa single tip, but more versatile as the timing, amount of force, andangle of force application can all be varied.

Another scenario where strain could be employed is when feedstock isheld by more than one bond to a tip. To reduce tip bond strength to thefeedstock, the bonding points can be pulled apart until the bonds arestrained by the desired amount. This is more easily illustrated in aslightly larger structure than a single adamantane, so that rigidity ofthe tip backbone can be used to create strain without excessivedeformation. For example, the native distance between two methyl groupsconnected by an oxygen (3HC—O—CH3) is about 2.36 A, and the angle isabout 110.7 degrees. However, due to the lattice spacing, thisconfiguration cannot be obtained on (111) diamond. If two adjacentcarbons on the (111) face of diamond each have a hydrogen removed, andan oxygen atom is then bound to those carbons, with a very smallstructure composed of 3 interlocked adamantanes (larger structures wouldlikely allow less deformation of the tip backbone), the oxygen becomesbound to the two carbons at an angle of about 87.8 degrees with thecarbons being spaced about 2.02 A apart. Clearly, this is a substantialdistortion of the minimal energy configuration and so if the oxygen isthe feedstock, it will require less energy to remove from the tipstructure than if it were bound in a configuration closer to its energyminima. Substitutions could be used to alter the diamond lattice spacingto increase or decrease the amount of strain created. An analogoustechnique could be used by a single feedstock moiety held by more thanone tip. The tip spacing could be used to adjust tip-feedstock bondstrength, and this could be changed on-the-fly if desired.

Note that with one single bond, as they are free to rotate, torsion isgenerally irrelevant. But, if a feedstock moiety was multiply-bonded, orone or more, e.g., double bonds (or any bond type not free to rotate),were used to bind the feedstock to one or more tips, or one or morepoints on a single tip, torsion could also be used to create strain, ascould any other well-known strain-inducing modifications.

Many of the same techniques could be employed on the workpiece. In somecases, modulating bond strength on the workpiece instead of, or inaddition to, the tip may be convenient. And, build sequence order can bechosen to create intermediate structures with strain if this alters thereactivity favorably.

It should be noted that creating strain and releasing strain are twosides of the same effect. If one considers a strained structure thedefault structure, releasing strain could be used to, for example,strengthen, instead of weaken, bonds. Further, strain levels need not bestatic. Levels of strain could be changed curing the course of areaction. For example, to increase tip affinity when picking upfeedstock, and then decreasing tip affinity when releasing feedstock.

FIG. 54 depicts various one way of creating adjustable strain, and henceaffinity, for feedstock. In FIG. 54a , a first tip (5401) is connectedto feedstock (5405) via bond (5403). A second tip (5402) is alsoconnected to feedstock (5405) via bond (5404). We assume this to be theminimum energy configuration. Various movements of the two tips wouldchange the bond angles and lengths, causing strain and thereby reducingthe affinity of the feedstock for the tips. For example, in FIG. 54b ,the two tips have been moved part, stretching and changing the angle ofthe bonds to the feedstock. In FIG. 54c , the two tips have been movecloser together, potentially compressing and changing the angle of thebonds to the feedstock. And, in FIG. 54d , one tip has been movedvertically with respect to the other, potentially resulting instretching of bond (5403) and compression of bond (5404), plus anglechanges. In a complete system, the tips would be attached to positionalmeans (not shown). It is possible that each tip has its own positionmeans. It is also possible that both tips reside on a single positionalmeans (and actually may be considered two halves of the same tip) inwhich case relative movement can still be caused in various ways. Forexample, the surface onto which the tips are affixed could be a piezoelement which can expand and contract. Or, changing temperature, charge,or other parameters could result in a conformation change in either thetips, or the surface to which they are affixed.

Workpiece Specification and Build Sequences

Many structures and reactions have been discussed herein, along withteachings which enable the creation of additional structures andreactions. However, to apply this information to the building of aworkpiece, it helps to define the workpiece in an atomically-precisemanner, and to define a build sequence which will create the workpiece.

A workpiece for mechanosynthesis can be defined by specifying each atomin the workpiece and its atomic coordinates, directly or indirectly (forexample, via an algorithm which generates the desired structure). Manycomputational chemistry programs allow the creation of models based onatomic coordinates, or algorithms to generate such coordinates.

Once the atomic coordinates have been specified, a build sequence can becreated that specifies the order in which each atom is to be added to,or removed from, the workpiece. Reactions that do not add or removeatoms are also possible, such as those that change the bonding structureof the workpiece, or if necessary, charge or otherwise alter tips. Thereactions must be ordered so that they result in the desired workpiece,while avoiding, for example, intermediate states prone to pathologicalreactions, or unstable structures that undesirably rearrange. Thesetopics are addressed in more detail below.

Process Flowcharts and Descriptions

To aid in the understanding of the general process of creating aworkpiece, FIGS. 55 through 58 illustrate embodiments of the inventionusing exemplary flowcharts. Note that many variations on these processesare possible, and even without changing the steps involved, one mightchange the decision logic or loop through some processes more than once.For example, to optimally design a workpiece for manufacturability(55-2) may require an iterative process where the workpiece design isrevised based on the outcome of subsequent steps or processes, such asthe reaction design process described in FIG. 56.

The process can be started in FIG. 55, which provides an overview of howa workpiece definition can be created, at step (55-1), “Create WorkpieceFunctional Specifications.” This step is similar to that for anytraditionally-manufactured product in that product requirements must bedefined before the product can be designed from an engineeringperspective.

Step (55-2), “Design Workpiece for Manufacturability” also has an analogin traditional manufacturing. The product must be designed with thelimitations of the manufacturing process in mind. In the case ofmechanosynthesis, this means that a device is preferably designed withelements and bonding patterns whose properties are understood, for whichtips and build sequences have been, or can be, designed and arecompatible with equipment capabilities, using geometries accessible tothe relevant tips, among other limitations which will be obvious tothose skilled in the art given the teachings herein.

Once the device has been designed, step (55-3) is to “Specify AtomicCoordinates of Workpiece.” That is, define each atom type and itsposition within the structure. This step may also include determiningbonding structure, as this step can be informative although technicallyredundant since the bonding structure may be fully specified via theatomic coordinates. This may be done in any molecular modeling orcomputational chemistry software with the appropriate capabilities, suchas HyperChem, Gaussian, GROMACS or NAMD.

Step (55-4) “Determine Reaction Reliability Requirements” involvesperforming an impact analysis of potential defects and the resultantestablishment of reaction reliability requirements. Although the goal ofmechanosynthesis is the production of atomically-precise products,unintended reactions can occur at frequencies which depend on factorsincluding the chemical reactions being used, the tip design, thereaction trajectory, equipment capabilities and temperature. For eachreaction one could analyze the most likely pathological side reactionsthat might occur and their impact upon the finished workpiece. Forexample, one could determine the impact of a feedstock atom failing totransfer, a feedstock atom bonding to a workpiece atom adjacent to theintended position, or the workpiece undergoing an unintendedrearrangement. The workpiece could be simulated with each potentialdefect, or more general heuristics or functional testing could be usedto determine the likely impact of possible errors in the workpiece.

As an example of how a defect could be insignificant in one context butnot in another, consider a simple part such as a structural beam: Asmall number of mistakes may not substantially affect the properties ofthe finished part, and may not affect the overall product, particularlyif the part has been over-engineered to allow for some defects. In sucha scenario, one might decide that some number of defects were tolerableand therefore require relatively low reaction reliability. On the otherhand, if the workpiece being constructed were, for example, asingle-molecule transistor that would not function correctly, or at all,if crucial atoms were misplaced, one might require a very low number(including 0) of defects.

One alternative to defect impact analysis is to require that eachreaction be reliable enough that it is statistically unlikely that thefinal workpiece contains any errors. This is quite feasible, as seenfrom the reaction reliability calculations presented herein. Also, theability to correct errors may have an impact on reaction reliabilityrequirements. If errors can be fixed, one might decide to reducereliability requirements and simply fix errors as they occur.

FIG. 56, which describes how a build sequence can be designed, beginswith step (56-1) “Determine Order of Reactions, Reaction Conditions andTrajectories.” Each atom, as specified in the atomic coordinates of theworkpiece, generally (but not necessarily since, for example, one coulduse dimers or larger molecules as feedstock) requires that a particularreaction be performed on the workpiece to deposit that atom. Abstractionreactions may also be required, as may be reactions which alter thebonding structure of the workpiece without adding or subtracting anyatoms.

There may be many different build sequences that would permit theconstruction of a particular workpiece. Steric constraints will be onedeterminant of the order in which atoms are added, as athree-dimensional workpiece requires adding atoms in an order whichpermits access by the necessary tools for later reactions. The stabilityof the intermediate structures should also be considered. For example,certain atoms, when left as radicals, might rearrange, forming undesiredbonds with adjacent atoms. In addition to a logical order to theaddition of atoms, other techniques can be employed to prevent undesiredrearrangement. For example, terminating atoms can be added to radicalsites to temporarily satisfy empty valances, or temperature can bereduced.

When a presumptive build order has been established, the build sequencemay be simulated to determine if it works correctly (56-2). The samesimulations can test reaction parameters including which tip to use,what temperature is required, and what trajectory a tip will follow. Ashas been previously noted, lower temperatures will favor accuracy, andfrequently the coaxial trajectory will enable successful reactions.

Note that, given that rearrangement and abstraction reactions may berequired in a build sequence, workpieces may require more reactions thanthe number of atoms in the finished workpiece. And, even if this werenot the case, workpieces with many atoms will generally require manyreactions. If the reactions are being implemented manually, this leadsto a substantial requirement for labor. Automating the reaction stepsmay therefore be desirable. CAD programs can be used to specify AFMtrajectories (Chen, “CAD-guided automated nanoassembly using atomicforce microscopy-based nonrobotics,” IEEE Transactions on AutomationScience and Engineering, 3, 2006; Johannes, “Automated CAD/CAM-basednanolithography using a custom atomic force microscope,” IEEETransactions on Automation Science and Engineering, 3, 2006), atomicforce microscopes that are programmable are commercially available, andprogramming languages or environments (e.g., LabVIEW) to controlscientific equipment are well known (Berger et al., “A versatile LabVIEWand field-programmable gate array-based scanning probe microscope for inoperando electronic device characterization,” Review of ScientificInstruments 85, 123702 (2014)).

Based on the outcome of the simulations, a decision is reached as towhether the reactions as specified are correct (56-3). If not, thesequence is revised. If so, the process proceeds to (56-4) where adecision is made as to whether any of the calculated reactions may posereliability concerns, for example, based on rearrangements or incorrectreactions that were seen during simulation in (56-2).

In (56-5) the reaction reliabilities can be calculated (for example, byenergy barrier calculations or Monte Carlo simulations). (56-6) is adetermination as to whether the proposed reaction reliabilities meetproduction quality needs, and, if the answer to (56-6) is no, theprocess proceeds to (56-7) where requirements are reviewed to see if thebuild sequence restrictions can be relaxed since they were not met. From(56-7) if the answer is yes, a new iteration is started at (55-4) todetermine revised reaction reliability requirements. If the answer to(56-7) is no, alternate reactions, reaction order, reactiontrajectories, or reaction conditions can be simulated (56-1) to find arevised build sequence that meets the reaction reliability requirements.If the answer to (56-6) is yes, the process continues in FIG. 57, step(57-1).

FIG. 57 describes a process for carrying out mechanosynthetic reactionsper a build sequence. Starting at (57-1) “Perform MechanosyntheticReactions,” the reactions determined in the build sequence are carriedout using SPM/AFM-like equipment, or other suitable equipment. This stepinvolves, whether manually or in a computer-controlled manner, using apositionally-controlled tip to perform each mechanosynthetic reaction inthe build sequence. This means picking up a feedstock atom from apresentation surface (or potentially a gaseous or liquid source offeedstock) and bonding it to the workpiece, or removing an atom from theworkpiece, or changing the bonding structure of the workpiece withoutadding or removing an atom. This step would also encompass otherreactions, including reactions not involving the workpiece, such as tiprefresh or pre-reaction feedstock manipulation as may be necessary.

Step (57-2) is a decision point. If the answer is “no,” testing is notrequired (for example, such as when the reactions being used arereliable enough that testing is superfluous), the process proceeds to(57-3). The action taken from (57-3) depends on whether all reactions inthe build sequence have been completed. If no, reactions are repeateduntil the answer is yes, at which point the workpiece is complete. Backat (57-2), if the answer were “yes,” testing is required, the processcontinues in FIG. 58, starting with step (58-1).

In FIG. 58, testing may done by, for example, scanning the surface of aworkpiece using AFM or SPM-like techniques and checking to see that theexpected structure is present. If no errors are found in (58-2), theprocess continues at (57-3). If an error is present at (58-2), adecision must be made in (58-3) as to whether the error is ignorable(e.g., not an error that would prevent the workpiece from functioning).If it is ignorable, the process again continues with (57-3), althoughthe build sequence may require adjustment if key atoms were moved as aresult of the error (not depicted). If the error is not ignorable, itmust be determined if the error can be fixed (58-4). This is largely aquestion of whether the tools and processes exist to fix the error.

Note that errors could be fixed in various ways, such as directlyreversing the last reaction if possible, or using abstraction tips toremove the local area of the workpiece entirely, paring the workpieceback to a point where the edges can be left in a correct and stableconfiguration. The build sequence would then be altered to fill back inthe removed area, before proceeding on with the rest of the sequence.

If the error can be fixed, this is done in (58-6) and the processcontinues with (57-3). If the error cannot be fixed, given that it waspreviously determined to be a crucial error, the build sequence must bestarted over (58-5).

The embodiment of the process shown in FIG. 58 assumes the ability todetect and fix errors (58-6). This is not necessarily the case, and thisflow chart represents only one possible process of implementingmechanosynthesis. For example, it is possible to desire testing withoutthe ability to fix errors, or at least not all errors, if only to knowthat the workpiece must be discarded and the process started anew, as in(58-5). It is also possible to forgo error checking completely, and thisis a reasonable solution especially for high-reliability reactions.Product requirements and process capabilities, among otherconsiderations, will determine which steps are actually used, and inwhat order.

A variation on the error correction described above is the use of“conditional” build sequences. Some reactions might be known to beerror-prone, having one or more pathological outcomes which cannot beprevented reliably. In this case, the creation of a branching, orconditional, build sequence can be useful. A conditional build sequencehas multiple paths, or sub-sequences, within it. The exact path chosenwill be determined by which structures result from the previousreactions. For example, assume that a build sequence reaches a reactionwhich is likely to have one of three outcomes. The exact outcome cannotbe controlled, but it can be accommodated by a build sequence whichcontains logic such as “If the product of reaction X is A, then do this.If the product of reaction X is B, then do something else. If theproduct of reaction X is C, then follow yet another path.”

Exemplary Build Sequences

Now that the process of designing a build sequence has been described,several exemplary build sequences, in addition to the half-Si-Rad buildsequence already described, are presented. The following sequences canbe used to create diamond (or with modification, diamondoid) structures.Reactions are logically grouped into sets of sequences which provide theability to initiate, extend, and terminate, rows in a diamond structure.In these particular sequences, the assumed starting surface is the 110face of diamond, although this is exemplary only, and other faces can bebuilt upon, and other surfaces used (e.g., diamond can also be built onSi, given the minimal lattice spacing mismatch).

These build sequences were computed using the representative densityfunctional method with the B3LYP/6-311G** basis set, which typicallyprovides a good tradeoff between accuracy and computational expense.Higher reaction accuracies could be obtained using morecomputationally-demanding techniques such as coupled clusters. (Lee,Scuseria et al., “Achieving Chemical Accuracy with Coupled-ClusterTheory,” Quantum Mechanical Electronic Structure Calculations withChemical Accuracy, Kluwer Academic Publisher, 1995) 4 degrees Kelvin wasassumed for this sequence (readily accessible with liquid helium)although the reactions would likely prove reliable at highertemperatures.

Reactions

The reactions in Table 2 are grouped into one of three functions: RowInitiation, Row Extension, or Row Termination. For example, to start anew row of diamond on a build surface, one would use the Row Initiationreactions, #1 to #11. To then extend that row, Row Extension reactions#12 to #17 would be used (as many times as necessary to achieve thedesired length). To terminate the row, Row Termination reactions #18 to#22 would be used.

Each set of reactions can be repeated as many times as necessary, atdifferent locations as appropriate, to build workpieces with variedgeometry. This is conceptually similar to how a 3D printer lays downlines or blobs of material which, in aggregate, build a desired shape.This analogy only goes so far however, because “3D printing” usingmechanosynthesis must take into account the varying chemical nature ofdifferent sites on a workpiece. For example, as the differentsub-sequences for building diamond show, placing the first carbon in arow is not the same as placing a middle carbon, or the carbon at the farend.

The tips used in these build sequences are described in detail elsewhereherein. They are: the Abstraction tip, the HDonation tip, the GermaniumRadical tip (GeRad), and the MeDonation tip. Additionally, while thedescriptions should make obvious the sequence of events, molecularmodels depicting the products and reactants of the reactions describedbelow can be found in US Patent Application 20160167970. Similarreactions and build sequences, along with a pyramidal exemplaryworkpiece, can be found in PCT Patent Application WO2014/133529.

TABLE 2 Exemplary Build Sequence Reactions # Description Tip RowInitiation Reaction Sequence 1 First step for row initiation, viaabstracting the hydrogen from the Abstraction outer edge carbon. 2Second step for row initiation, via donating the radical methyl groupMeDonation to the radical outer edge carbon. 3 Third step for rowinitiation, via donating a hydrogen to the radical HDonation outer edgemethyl group. 4 Fourth step for row initiation, via abstracting thehydrogen from the Abstraction surface carbon adjacent to the outer edgemethyl group. 5 Fifth step for row initiation, via donating a radicalmethyl group to MeDonation the radical surface carbon adjacent to theouter edge methyl group. 6 Sixth step for row initiation, viaabstracting a hydrogen from the Abstraction outer edge methyl group,allowing radical-radical coupling between the carbon site of the outeredge methyl group and the adjacent radical methyl group to form a6-member ring. 7 Seventh step for row initiation, via abstracting ahydrogen from a Abstraction secondary carbon within a 6-member ring. 8Eighth step for row initiation, via abstracting a hydrogen from aAbstraction secondary carbon adjacent to a radical carbon both within a6- member ring, allowing radical-radical coupling between the twoadjacent secondary radical carbons forming a C═C double bond. 9 Ninthstep for row extension, via abstracting a hydrogen from the Abstractionsurface carbon adjacent to the 6-member ring. 10 Tenth step for rowextension, via donating a radical methyl group. MeDonation On approachof the tip to the surface, the radical methyl group breaks into the C═Cdouble bond of the 6-member ring, allowing for subsequentradical-radical coupling of the radical surface carbon with the radicalmethyl carbon on retraction of the tool from the surface. 11 Final stepfor row extension, via donating a hydrogen to the radical HDonationsecondary carbon. Row Extension Reaction Sequence 12 First step for rowextension, via abstracting a hydrogen from the Abstraction surfacecarbon adjacent to the cage. 13 Second step for row extension, viaabstracting a hydrogen from the Abstraction secondary carbon within thecage adjacent to the surface radical carbon, allowing forradical-radical coupling creating a strained tertiary carbon site. 14Third step for the row extension, via abstracting a hydrogen fromAbstraction the strained tertiary carbon. 15 Fourth step for rowextension, via donating a radical methyl group MeDonation to thestrained radical tertiary carbon. On retraction of the tip from thesurface, the bond between the strained tertiary carbon and the surfacecarbon breaks with preference to form an unstrained C═C double bond. 16Fifth step for row extension, via approaching the secondary carbon GeRadof the C═C double bond with tip, allowing the radical surface carbon tobreak into the C═C double bond thereby forming a C—C single bond betweenthe primary carbon and the surface carbon. 17 Final step for the rowextension, via saturating the radical tertiary HDonation carbon. RowTermination Reaction Sequence 18 First step for the row termination, viaabstracting a hydrogen from a Abstraction tertiary carbon. 19 Secondstep for row termination, via abstracting a hydrogen from Abstractionthe secondary carbon adjacent to the radical tertiary carbon, allowingradical-radical coupling to form a strained C═C double bond. 20 Thirdstep for row termination, via donating a radical methyl group MeDonationto the secondary carbon of the strained C═C double bond. On retractionof the tip from the surface, the position of the radical methyl groupfacilitates the migration of a hydrogen from the outer edge carbonthereby saturating the methyl group and leaving a radical outer edgecarbon. 21 Fourth step for row termination, via donating a hydrogen tothe HDonation radical tertiary carbon. 22 Final step for rowtermination, via abstracting a hydrogen from the Abstraction methylgroup, allowing radical-radical coupling to occur between the radicalmethyl group and the radical outer edge carbon, closing the row.Differentiating Mechanosynthesis Products

It should be noted that, while a pyramidal workpiece is mentioned here,the reaction sequences provided can make many other shapes. In general,workpieces can be virtually any shape permitted by the chemistry of theworkpiece, though some shapes and substitutions may require the designof additional reactions. While shapes such as pyramids, cuboids,cylinders, spheres, ellipsoids and other simple geometric shapes canobviously be made, they are perhaps not the most interesting or mostuseful examples of what can be built with mechanosynthesis. This is fora variety of reasons, including the fact that their simplicity limitstheir functionality (although different parts can be combined to addressthis issue), and because at least some of these shapes can beapproximated, even if not in an atomically-precise manner, by othertechnologies. For example, it may be possible to grow some simple,approximate shapes using chemical vapor deposition.

What are perhaps more interesting cases are where the workpiece is not asimple shape, or any periodic shape derived directly from its crystalstructure (which might permit its manufacture by CVD, self-assembly, orsome other known process). We will refer to such workpieces as being“aperiodic”, and aperiodic workpieces are interesting because as far aswe know, mechanosynthesis is the only way to produce such workpieces.For example, consider an arbitrary shape such as the outline of a car(to use a familiar shape, if not a relevant scale). Even if CVD could beused to grow atomically-precise crystals, there is no way it could beused to achieve such an irregular shape. Also included in aperiodicworkpieces would be workpieces that may largely be periodic, but whichhave aperiodic substitutions. For example, consider a diamond cube,perfect and regular in all respects except that nitrogen vacancies havebeen placed in specific locations. Again, this would be impossible tocreate via CVD, or any other technology of which we are aware besidesmechanosynthesis, yet this could be a very useful workpiece forrealizing a quantum computer. The vast majority of parts, whethermechanical or electronic, used in devices today, are aperiodic. Beingaperiodic is the rule rather than the exception, and while such partsare easily manufactured at the macro-scale using subtractivemanufacturing (e.g., machining) and other techniques, it is verydifficult to manufacture such parts with atomic precision. In most caseswe would say that it is impossible without mechanosynthesis.

Another way to view the difference between mechanosynthesis products andother natural or synthetic products is to compare some other aspects oftheir makeup aside from periodic versus a periodic. Specifically, it isinformative to consider stiffness, bonding structure, size, andcomplexity (which can be related to, but is not the same as periodicity,or lack thereof).

Large numbers of natural and synthetic chemical structures, andsynthesis pathways, are known outside of mechanosynthesis. And, giventhese known structures and synthesis pathways, the manufacture of manymore structures would be possible. Some of these structures are large(as molecules go), some are stiff and highly-bonded, some have strainedbonds, some are atomically-precise, and some, by various measures, couldbe considered complex. However, no natural or synthetic structureprepared without the aid of mechanosynthesis, possesses all of thesecharacteristics.

For example, DNA of essentially arbitrary length and sequence can beprepared using conventional techniques. And, given that DNA need not besimply a repetition of the same monomer, by some measures DNA sequencescould have high complexity. However, DNA is essentially a floppy,one-dimensional polymer. Although DNA can fold into 3D structures, eventhen, DNA is not stiff or highly-bonded.

Large, three-dimensional polymers can be synthesized. For example, adendritic polymer of 2×108 Daltons has been synthesized (Zhang, Wepf etal., “The Largest Synthetic Structure with Molecular Precision: Towardsa Molecular Object,” Angewandte Chemie International Edition, 3,WILEY-VCH Verlag, 2011). However, the ability to precisely control thecomposition of such polymers is lacking, and they tend to be relativelysimple polymeric sequences which have been joined in a manner thatallows them to assume a three-dimensional shape. The dendritic polymersynthesized by (Zhang, Wepf et al., “The Largest Synthetic Structurewith Molecular Precision: Towards a Molecular Object,” Angewandte ChemieInternational Edition, 3, WILEY-VCH Verlag, 2011) is not stiff,highly-bonded, or complex, and subsequent work on error rates at variouspoints in the molecule indicate that it is not atomically-precise.

Structures consisting of multiple adamantane units in randomconfigurations have been purified from petroleum. These structures arestiff and highly-bonded. Additionally, various chemical processes areknown to make modified or functionalized adamantane (Szinai, “ADAMANTANECOMPOUNDS,” U.S. Pat. No. 3,859,352, United States, Eli Lilly andCompany (Indianapolis, Ind.), 1975; Baxter, “Adamantane derivatives,”U.S. Pat. No. 6,242,470, United States, AstraZeneca AB (Sodertalje, SE),2001). However, the adamantane aggregates obtained from natural sourcesare connected randomly, and so the chances of finding any particulararrangement of adamantanes as the size of the molecule grows becomesvanishingly small. In practicality, these molecules are neither largenor atomically-precise. The functionalized adamantanes used in thepharmaceutical industry are atomically-precise, but they are not largeor highly-bonded (since such molecules tend to be, for example, a singleadamantane connected to a long, flexible side chain).

Diamond, whether natural or synthetic (e.g., grown via chemical vapordeposition) is neither complex, being (with the exception of errors) auniformly repeated three-dimensional polymer of adamantane, noratomically-precise, as even the most perfect such diamond has flaws atthe atomic level.

With respect to strained bonds, the creation of individual strainedbonds is routine in chemistry, and molecules like cyclopropane andcubane exemplify the structures that can be created with strained bonds.Larger structures containing many strained bonds also exist, e.g.,Fullerenes of various configurations. While the specific mechanisms offormation are very different, there is a commonality between thesynthesis of cyclopropane, cubane, Fullerenes, and other strainedmolecules in that there are energetically-feasible sequential reactionpathways leading from the initial reactants to the final product.

However, there are classes of strained structures for which this is nottrue; there is no practical pathway from the component atoms ormolecules to the final product using only conventional chemistry. Toconceptually illustrate this principle, consider a stiff, rod-shapedmolecule. Now, bend the rod into a circle and connect the ends. Ahoop-shaped molecule is formed. While hoop-shaped molecules abound,including all the cycloalkanes, and the many other cyclo-polymers, theformation of such structures rely upon some fairly restrictiverequirements. The main requirement for the formation of these strainedstructures is that the two ends can be brought close enough together sothat they can be bonded together, changing the molecule from a linearstructure into a circular structure. The two ends of the linear moleculecan be closely approximated in a variety of ways. For example, themolecule can be very small to begin with, so that even if the moleculeis straight, the two ends are both within reach of a single reaction.Or, the molecule can be flexible enough that it can bend into thenecessary configuration. Or, the linear molecule could have an inherentcurve to it, making it already a partial hoop and thereby leaving only asmall gap to bridge.

But, consider a class of molecules that do not meet these requirements.A long rod, if stiff enough, even if somewhat curved, with a substantialgap between its ends, cannot be made into a hoop through conventionalchemistry techniques. Similarly, a stiff two-dimensional molecule (e.g.,a plane of diamond just one or two adamantane layers thick) will beunable to curl into a tube structure, both because of its stiffness, andpossibly because multiple bonds would have to simultaneously form tohold the new tubular structure in place—a statistically unlikely event.

A stiff, long, potentially wide, structure with two sides which are,atomically speaking, far apart, but which need to be brought together tothen undergo a bonding reaction to form a stable hoop or cylinder maysound like a very contrived class of structures. It is not. For example,it is exemplary of many of the bearing designs which have been proposedfor nano-devices, where an axle revolves inside a stiff cylindrical ringor tube. Mechanosynthesis can form such structures in a variety of ways,such as by using force to approximate the necessary ends, or by buildinga temporary jig around the structure that forces intermediate structuresinto the necessary shape (and which can then be removed once the desiredstructure is complete).

These are only examples. Comments similar to those about DNA anddendritic polymers apply to other polymers as well, comments similar tothose about adamantane apply to the existence or synthesis of otherstructures, comments similar to those made about diamond apply to othercrystals, and certainly rod or plane-shaped structures that need to befolded into hoops or cylinders are not the only example of howpositional control allows the formation of structures which could not bemade via conventional chemistry due to geometric issues.

Another problem with traditional chemical synthesis methods, geometryissues like those described above aside, is that there is no way todifferentiate multiple sites which have similar or identical chemicalproperties, and yet the end product requires that they be treateddifferently. Linear polymer synthesis (e.g., DNA synthesis) is anexception, since it is possible to work only at one or a few specificlocations (e.g., the ends) of a growing one-dimensional polymer, butthese polymers are not stiff, or amenable to the formation of precise,highly-bonded three-dimensional structures.

Once molecules become two or three dimensional, the problem ofchemically-equivalent sites at different locations appears. For example,consider a perfectly flat plane of diamond, onto which a structure is tobe built. Reactions are known which can add additional carbon (or other)atoms to diamond; this is the basis for CVD-based growth of diamond.However, with the exception of the edges and corners of the plane, whichhave different bonding structures by virtue of not having the samenumber of neighboring carbon atoms as the atoms away from the edge, allthe sites on the surface of the plane are essentially chemicallyequivalent. There is no way that CVD, or any non-positional techniquecan, for example, start adding new atoms to the plane at arbitrary,atomically-precise coordinates.

This concept of multiple chemically-similar or chemically-identicalsites is the reason that three-dimensional dendritic polymers have asimple, repetitious structure: Whatever reaction happens to one branchtends to happen to the equivalent sites on all branches. Beyonddendritic polymers, this general concept is one of the main reasons thatsynthetic chemistry cannot create arbitrarily large and complexstructures.

Certainly mechanosynthesis could be used to make products including DNAand other polymers, small molecules, or repetitious structures of lowcomplexity. In fact, such products would be superior in some ways. Forexample, products of 100% purity could be created, potentially improvingthe properties of the product, as well as eliminating waste, and theneed for purification steps.

However, when speaking of the possible products of mechanosynthesis,these are not the most important cases since such products, even ifinefficiently or imperfectly, can already be created. The more importantcases are those structures which cannot reasonably be created orobtained by other means. For the aforementioned reasons, these tend tobe structures that are atomically precise, large, highly bonded, andcomplex. Such structures may occur with or without strain; the presenceof at least some kinds of strain makes it even more unlikely that anymethod other than positionally-controlled chemistry can create such astructure.

Reliability

Reliability is an important consideration in the design of buildsequences for multi-atom workpieces. Reaction reliability can beachieved in a variety of ways, including use of reactions with energybarriers sufficient to prevent spontaneous reactions at a giventemperature, reactions designed to avoid pathological side reactions(for example, by approaching a workpiece using a trajectory that favorsonly the desired reaction, or by ordering a build sequence to avoidleaving unsatisfied valences in self-reactive positions), or theintroduction of a testing step during mechanosynthesis. These topics arediscussed in more detail below.

In some cases, primarily with respect to hydrogen due to its low atomicmass, tunneling can contribute to reaction error. These errors can bereduced with slight modifications in build sequences to avoidproblematic situations. Also, deuterium could be used in place ofstandard hydrogen. Deuterium's different mass and Van der Waal's radiusalso has effects on reaction rates (the kinetic isotope effect),vibrational frequencies, torsional coupling and other properties. All ofthese effects may be exploited by choosing to use hydrogen or deuteriumon a case by case basis. Note that in general, any isotope of an elementcould be used where its properties are advantageous, and the ability topositionally control isotopes of an element may useful, just as thepositional control of different elements is useful.

Reaction Barriers and Temperature

Note that equipment capabilities could have an effect on reactionreliability. For example, the error in a positional means is unlikely tobe zero. However, it is well within the limits of conventional atomicmicroscopy technology to attain high enough positional accuracy that itessentially becomes irrelevant. With equipment that can position a tipwith a precision of, e.g., <20 pm, temperature becomes the dominatingvariable in reaction reliability. As the positional means become lessaccurate, reaction reliability suffers regardless of temperature, andfor example, positional errors of 50 pm or more will substantiallyreduce the reliability of many mechanosynthetic reactions. Those skilledin the art will understand how to incorporate such equipment limitationsinto reaction reliability calculations, if necessary. For exemplarypurposes, only temperature is considered in the following example ofcalculating reaction reliability.

One of the advantages of mechanosynthesis is that it facilitatesspecific, desired reactions by using directed mechanical force toovercome reaction barriers. In conventional chemistry, reaction barriersor energy deltas are often overcome by thermal energy. However, thermalenergy is nonspecific and facilitates desired and undesired reactionsalike. Reducing temperature decreases the thermal energy available tocause non-specific reactions. This reduces the likelihood ofpathological side reactions while directed mechanical force, even at lowtemperatures, still facilitates desired reactions.

The Arrhenius equation and other principles of thermodynamics andcomputational chemistry may be used in conjunction with data on netenergy differences and energy barriers to determine the reliability of agiven reaction at a given temperature. For example, the followingMathematica v8 code may be used to determine reaction reliability at agiven temperature when considering the net energy difference between twostructures (e.g., the before and after workpiece structures):

Code Listing 1:

(**calculate reliability of a reaction at a given temperature**)

(**Define Constants and Unit Conversions**)

(**Boltzmann constant=1.38*10^-23 J/K**)

-   -   boltzmann=1.381*10^-23;        (**convert eV to Joules**)    -   jouleBarrier=barrier*1.6*10^-19;        (**inputs for specific reaction**)    -   (**reaction barrier in eV**)    -   barrier=Abs[−0.6418];    -   (**temp in Kelvin**)    -   temperature=300;        (**Calculate Probability of Failure**)    -   probability=NumberForm[Exp[−jouleBarrier/(boltzmann*temperature)],        4]        Reliability in Build Sequences

The reliability of reactions across a build sequence can provide one wayof assessing the statistical error rate. And, depending on which, or howmany, errors are considered significant enough to compromise workpiecefunction, these data can then be used to assess workpiece yield (orperformance, in a scenario where workpieces do not simply pass/fail aquality check and the effect of certain errors on workpiece function areknown) in a manufacturing setting. This is most easily explained byexample.

Consider a workpiece which requires 10^6 reactions to create. For thesake of simplicity, assume that each of these reactions are identical intheir energy barrier to a pathological reaction (an error), and that thebarrier is 0.2 eV. Another assumption is that simulations, practicalexperience, or other information provide guidelines as to how manyerrors, on average, may be present before a workpiece is deemeddefective. Arbitrarily, since this would vary with the workpiece design,a limit of 10 errors is used for this example. Which is to say, aworkpiece having between 0 and 10 errors is acceptable, while aworkpiece having over 10 errors will be rejected as defective. Finally,(again, arbitrarily to demonstrate the logic, since this number willvary depending on the business and technical requirements) a yield of atleast 90% is required.

Since an error is presumed to be a rare event, error occurrence ismodeled as a Poisson distribution. The problem then becomes one ofdetermining 1, the number of expected events, where the CumulativeDistribution Function is equal to or greater than 0.90 (a 90% yield)when the number of events is 10 (the maximum number of tolerableerrors). In this case, 1 is 7. Meaning, if one expects, on average, that7 errors will occur during the build sequence, then 90% of the time, nomore than 10 events will occur. So, the expected number of errors mustbe <=7. Since the hypothetical workpiece requires 10^6 reactions tobuild, the threshold for mistakes is 7/10^6. Using the equations hereinto solve for the maximum allowable temperature to attain this accuracygiven a 0.2 eV barrier, the answer is about 195 degrees Kelvin.Obviously this number can change depending on actual reaction barriers,manufacturing requirements, equipment capabilities, and other factors.

Note that these calculations assume that temperature is the sole factorlimiting reliability. As previously noted, there may be other sources oferror, caused by factors such as positional uncertainty in theequipment, or Hydrogen tunneling, and these could be factored in whenassessing an actual manufacturing process. Also, note the assumptionthat errors are statistically independent. Error independence isunlikely in some scenarios, since a missing or mis-bonded atom may causesubsequent problems when placing neighboring atoms. However, this is notnecessarily the case, and regardless, the issue can be made irrelevantby requiring an error rate approaching 0%.

Temperature and reaction barriers aside, considering the statistics ofthe case where zero errors is the requirement provides a way to comparethe literature processes to the reliability requirements needed for thecreation of more complex workpieces. The literature often describesexperiments involving between one and about twelve reactions. Theliterature does not report error rates, but theoretically, how reliablemust the reactions be to perform, for example, twelve reactions with noerrors? A simple calculation (Reliability #Reactions=Yield) shows that90% reliability for each reaction would give a 28% yield. That may be anacceptable, or even excellent, yield for a laboratory process, but afairly poor yield for an industrial manufacturing process, and that iswith only 12 reactions.

If the workpiece requires 20 reactions, a 90% reliability for eachreaction gives a yield of 12%. At 50 reactions, 90% reliability providesa yield of only 0.5%. By 100 reactions, 90% reliability is no longerreasonable as an error-free workpiece would almost never be created. For100 reactions, the reliability needs to be more in the 95-99% range.And, for 1,000 reactions or more, assuming that a yield of more than afew percent is desired, the reliability needs to approach 100%.

Note that some reactions will be abstraction or rearrangement reactions,while some will be addition reactions which may add more than one atomat a time. On average, the number of reactions probably exceeds thenumber of atoms in a given workpiece, but the order of magnitude will bethe same, so for ease of discussion we will assume that a workpiececontaining 20 atoms takes about 20 reactions, a workpiece containing 50atoms takes about 50 reactions, a workpiece containing 100 atoms takesabout 100 reactions, and a workpiece containing 1000 atoms takes about1000 reactions, and so on.

Clearly, error rates that are acceptable for workpieces requiringtrivial numbers of reactions are unsatisfactory for building morecomplex workpieces. Of course, this statement comes with a number ofassumptions, such as no error correction processes, and little tolerancefor errors in the finished workpiece. But, in general, this illustratesthe need for rationally-designed build sequences, based on reactions ofknown reliability, that permit reliability far in excess of thatevidenced in the literature (but well within the capabilities of thereactions reported herein).

Of course, some useful build sequences are quite short. For example,depending on whether the starting point is a dehydrogenated Si surfaceor a brominated Si surface, the half-Si-Rad build sequence describedherein is only 11 to 15 steps long. Similarly, initiating a new row on adiamond surface takes 11 reactions, extending the row takes 5 steps, andterminating a row takes 6 steps (ignoring that such steps will oftenneed to be repeated—while this would frequently be the case, it cannotbe said to always be the case). Clearly, some build sequences may bebetween 5 and 10, or between 10 and 20, steps long and still accomplishsomething of value. In such circumstances, reliability requirements forthe individual reactions might be lower and still result in success somereasonable percentage of the time, as opposed to build sequences whichhave, e.g., 20 to 50, 50 to 100, 100 to 1,000, or more, steps.

What is claimed is:
 1. A method of creating a build sequence for aworkpiece comprising: a. at least one of the steps of, usingcomputational chemistry algorithms to simulate mechanosyntheticreactions at a given temperature and with realistic equipmentlimitations to compute a degree of reliability for said mechanosytheticreactions, and choosing pre-computed mechanosynthetic reactions from alibrary wherein the degree of reliability of such reactions has alreadybeen computed; and b. determining a set of, and order of, the computedmechanosynthetic reactions that will build the workpiece with a desireddegree of reliability.
 2. The method of claim 1 wherein the order inwhich said mechanosynthetic reactions are to be performed is determinedat least in part by steric considerations.
 3. The method of claim 1wherein the order in which mechanosynthetic reactions are to beperformed is determined at least in part to avoid undesiredrearrangements in intermediate workpiece structures.
 4. The method ofclaim 1 wherein one or more of the mechanosynthetic reactions use aplurality of tips simultaneously.
 5. The method of claim 1 wherein thecomputational chemistry algorithms simulate the use ofatomically-precise tips.
 6. The method of claim 5 wherein theatomically-precise tips are comprised of adamantane-like structures. 7.A method of creating a build sequence for a workpiece, comprising: a.defining the atomic coordinates of the workpiece in a computer memoryaccessible by a computer; b. defining the positional error in apositional device used in the workpiece manufacturing process such thatthe defined positional error is accessible to the computer; and c. usingcomputational chemistry algorithms in conjunction with the computer todetermine an order and set of mechanosynthetic reactions, that, giventhe positional error in the positional device used in the workpiecemanufacturing process, can be used to build the workpiece to a knowndegree of reliability.
 8. The method of claim 1 further comprising thedetermination of a revised or conditional build sequence which willcorrect errors which occur in said mechanosynthetic reactions.
 9. Amethod of employing a mechanosynthetic build sequence, comprising: a.loading a mechanosynthetic build sequence into a computer memory that isconnected to a computer, said build sequence comprising an orderedsequence of mechanosynthetic reactions for which the degree ofreliability in positioning feedstock at a specific site, at a giventemperature and with realistic equipment capabilities includingsub-angstrom positional accuracy, has been calculated, the buildsequence having been determined capable of creating a workpiece with adesired degree of reliability, wherein said computer is connected to apositional device that meets the equipment capabilities used tocalculate reaction reliability; and b. operating said positional deviceunder control of said computer at a temperature no greater than thegiven temperature used to calculate reaction reliability so as to carryout a plurality of mechanosynthetic reactions from said build sequence.10. The method of claim 1 wherein the workpiece has at least 100 atoms.11. The method of claim 10 wherein the workpiece is aperiodic.
 12. Themethod of claim 10 wherein the workpiece is three-dimensional.
 13. Themethod of claim 7 further comprising the determination of a revised orconditional build sequence which will correct errors which occur in saidmechanosynthetic reactions.
 14. The method of claim 7 wherein the orderin which said mechanosynthetic reactions are to be performed isdetermined at least in part by steric considerations.
 15. The method ofclaim 7 wherein the order in which mechanosynthetic reactions are to beperformed is determined at least in part to avoid undesiredrearrangements in intermediate workpiece structures.
 16. The method ofclaim 7 wherein one or more of the mechanosynthetic reactions use aplurality of tips simultaneously.
 17. The method of claim 7 wherein thecomputational chemistry algorithms simulate the use ofatomically-precise tips.
 18. The method of claim 7 wherein the workpiecehas at least 100 atoms.
 19. The method of claim 18 wherein the workpieceis aperiodic.
 20. The method of claim 18 wherein the workpiece isthree-dimensional.